Stephen Fitzpatrick – If it seems Indonesia's air safety record has improved since the Garuda crash two years ago that claimed 21 lives and has now seen pilot Marwoto Komar sentenced to jail, it is an illusion at best. Less than two hours after yesterday's decision, a military plane crashed into a hangar at an airbase in West Java, killing 24 crew.

And while there has not been a commercial air disaster on such a scale as the Garuda crash since that morning, a closer inspection of the lessons learned reveals structural issues affecting Indonesian aviation. After Marwoto variously blamed wind and mechanical problems during landing, and his co-pilot Gagam Saman Rochmana changed his story on the stand to say that buffeting had caused him to black out during the fatal final seconds, the experienced 45-year-old captain has been found guilty of causing death by negligent flying, and sentenced to two years in jail.

It's a historic decision, marking one of the few times an airline captain has been found guilty of a criminal offence in relation to a crash – and the first such time in Indonesia – but Marwoto is far from the only weak spot in Indonesian aviation.

The facts of the day are well known and were repeated in the summing up in court yesterday in the central Java city of Yogyakarta, where the tragedy occurred.

Soon after dawn on March 7, 2007, Marwoto, having ignored a growing deviation from his filed flight plan while still at least 10 minutes from Yogyakarta's airport, then a series of automated cockpit voice warnings and finally the shouted urgings of his co-pilot, brought his Boeing 737-400 in at twice the correct speed.

The jet bounced three times on hitting the runway, then burst through a fence, across a military access road and into a paddy field, where it caught fire.

Among the 21 who died were five Australians: Australian Federal Police officers Brice Steele and Mark Scott, AusAid country head Allison Sudradjat, diplomat Elizabeth O'Neill and The Australian Financial Review journalist Morgan Mellish. The Sydney Morning Herald reporter Cynthia Banham was seriously injured, losing both legs.

All were travelling in connection with a visit to the ancient royal city by then foreign minister Alexander Downer.

But air accident investigators say it's never a single thing that causes a crash; rather, there is a build-up of factors, most of which could have been addressed individually.

Had it not been for the access road where there should have been a safety run-off area, Marwoto's inexplicable decision to land despite all the warnings might not have produced the torn wings, ruptured fuel tanks and subsequent inferno that caused most of the 21 deaths.

Had airport emergency services been adequately equipped and maintained, and had they been able to get across the access road to where the jet was burning, more lives could have been saved. Instead, firefighters tried in vain to direct their under-pressurised hoses from more than 100m away, hindered further by spectators riding motorcycles across them.

The Indonesian Pilots Federation says Marwoto should never have been taken to a criminal trial but instead should have been subject only to industry and civil sanctions, as are most pilots who survive such incidents.

"His licence has been revoked, that's the heaviest penalty possible for a pilot, there's nothing above that," federation spokesman Manotar Napitupulu said last week.

Critics of the stranglehold pilots' associations worldwide have over the issue of criminal prosecutions say pilots should be subject to the same duty of care and liability issues as other professionals, and to criminal prosecutions where relevant. But pilots insist judges and juries are not competent to examine negligence in their industry and insist other failings, such as maintenance, industry standards and company policy – including fuel quota regimes – have a part to play in accidents.

The key question is whether Indonesia has done anything about addressing the broader issues of transport safety that the Garuda crash revealed. The answer is a resounding no. It's not for want of trying, including through a $24 million, three-year fighting fund from Australia designed to improve our largest neighbour's ability to turn around its appalling safety record.

But barely a week goes by without an air traffic incident of some kind. Yesterday's crash of a military Fokker 27 at Bandung, killing 24, came two weeks after a plane operated by the second-string national airline, Sriwijaya Air, was forced to make an emergency landing after an engine failed at 610m. That Jakarta-bound 737-200 had barely left the runway at Tanjung Pinang, on Bintan island south of Singapore, when the pilot requested urgent clearance to divert to nearby Batam island.

Days earlier, a passenger jet operated by Lion Air slid off the runway at Jakarta's airport while landing in heavy rain, breaking the front landing gear and left wing. Luckily there were no injuries among the 158 passengers and six crew, but the extraordinary thing is how commonplace and accepted such incidents have become.

Indonesian airlines have pariah status internationally almost everywhere outside Asia except for Australia, and there have long been claims that exception exists only because of the political turmoil a ban on Indonesian carriers flying to Australia would produce. Not least, presumably, would be a reciprocal Indonesian attack on Australian airlines, and with the global financial crisis seeing Australian consumers increasingly shifting to low-cost, short-haul flights such as the traditional holiday in Bali, the economic effect would be deep and lasting.

A European Union ban on all Indonesian airlines has been in place since July 2007; it was prolonged indefinitely last June. The edict is not restricted to any one company; the flagship carrier, Garuda, had to gain a special exemption to fly President Susilo Bambang Yudhoyono and his entourage to London last week for the G20 meeting. It was the first Indonesian flight to Europe since the restriction was imposed in response to the 2007 Garuda crash and to an earlier Adam Air disaster, when a plane disappeared off Sulawesi island on New Year's Day 2007 as its disoriented pilots misread vital instrumentation and mistakenly turned off the autopilot. All 102 people on board were killed.

Observers do not expect the EU ban to be lifted before the second half of this year, although Garuda has ordered 10 widebody Boeing 777-300 jets with which it hopes to resume services to Amsterdam next year. Indonesia's airlines are also accorded the US Federal Aviation Authority's lowest rating.

It's a precarious position for the industry to be in, since with the global economic downturn air travel across Southeast Asia is a key growth market and Indonesia's figures are especially healthy. Transport Ministry data shows domestic air travel leapt from about 10 million passengers annually six years ago to more than 40 million today.

The Australian assistance package, signed by Transport Minister Anthony Albanese in Jakarta in January last year, is meant to improve safety across all transport sectors. The troubled maritime sector, which features regular rainy-season sinkings of overcrowded passenger ferries, is also a beneficiary under the program.

The package is strictly about capacity building, not, for instance, addressing crucial concerns such as the access road at Yogyakarta, which still remains in place, partly due to squabbles over who ought to pay for its relocation. Most airports across Indonesia have similar basic structural defects of various kinds.

"This capacity building involves accident investigation training, also training flight safety inspectors with regard both to operational and technical matters," says Transport Ministry spokesman Bambang Ervan.

Indonesia's National Transport Safety Committee (KNKT) also has acquired technology recently that could aid technicians trying to pull information off black-box cockpit voice recorders and flight data recorders that can pinpoint what went wrong in the final moments of a doomed journey.

"Although we cannot yet use (these devices), we hope we will be able to by the end of this year or the beginning of next, but because they are still new, the technicians and analysts are still being trained in Australia," Ervan says.

He says Indonesia is anticipating the day it can perform credible investigations into its own disasters, a process with which, in the case of the Adam Air and Garuda crashes, it was heavily reliant on outside help. The Australian Transport Safety Bureau, for instance, played a leading hand in preparing the accident report into the Garuda crash.

The head of the bureau's Indonesian equivalent agency, Tatang Kurniadi, admitted a month ago his office was too understaffed to produce adequate investigations into most incidents and that some matters remained unexamined.

"This is a matter of human resources and skills," Kurniadi said at a transport safety workshop in Jakarta, adding that his office had just 39 investigators and that, as these were hired on a contract basis, they were not paid regularly.

Industry analyst and Angkasa (Aerospace) magazine editor Dudi Sudibyo says any recent improvements in Indonesia's airline sector fall well below requirements.

"The big problem is human resources," he says. "We are short of safety inspectors and if we want to employ more of them it's going to take time and money. And air traffic controllers are underpaid, really underpaid, even though they have (the lives of) thousands of passengers in their hands. How can they work at their best if they have to be thinking about putting food on the table? Salaries, improving prosperity, is important."

The situation came to a head last month with the announcement that 26 air traffic controllers would take leave from the state airports operator PT Pura Angkasa to work abroad, most of them in the Middle East. With an estimated nationwide air traffic controller shortfall of about 700, it was not a good omen.

Likewise, pilot retention rates are appalling. The expansion worldwide of air travel markets means the best Indonesian pilots rarely fly for Indonesian carriers.

Garuda chief executive Emirsyah Satar admitted in an interview with The Australian last year it was difficult for his airline – the country's most successful – to pay salaries attractive enough to keep top pilots.

From Sudibyo's perspective, there is a light on that horizon with the opening last month of a pilot training school in Bali. "The first 40 graduates from that school, (half) will go straight into service at Garuda, and the (rest) at Lion," he says. "So there is an improvement coming from the private sector; we can't just look to governments." But it may all be too little, too late. Sudibyo admits that with new flying schools opening, there is no way existing capacity can meet the demand of an aggressively expanding industry.

And while carriers such as Garuda and Lion, as well as the former military-owned Mandala, are modernising their fleets, there are still plenty of clunkers among the country's 200 aircraft, as anyone who travels the country knows.

[Stephen Fitzpatrick is The Australian's Jakarta correspondent.]