Tom Hyland – Despite a publicised handover of a handful of weapons by rebel soldiers, mystery over the whereabouts of thousands of police guns is delaying efforts to resolve East Timor's security and political crisis.

Australian peacekeepers have yet to do an audit of the 4000 police firearms, many of which are believed to have been given to civilian militants allied to factions in the ruling Fretilin party.

The Sunday Age believes that Australian forces have accounted for most of the weapons held by the army. A rebel force led by Major Alfredo Reinado handed over a further 16 firearms to Australian peacekeepers on Friday.

While that handover was reported as a breakthrough, key issues over the massive police armoury created by controversial former interior minister Rogerio Lobato remain unresolved.

Human rights groups in Dili say thousands of people in makeshift refugee camps are reluctant to go home until they are confident police guns have been taken from militants armed by Mr Lobato, who controlled the police until he resigned last month.

An Australian-supervised audit of the police armoury, which includes automatic weapons normally used by military forces, has yet to begin. An Australian Defence Force spokesman refused to say how many police weapons had been recovered since Australian troops arrived in East Timor three weeks ago.

He said more than 1000 firearms had been handed in or confiscated, but was unable to say whether these were police or army weapons. Nor was he able to say how many weapons were unaccounted for.

Australian forces have done a stocktake of army weapons. It is being checked against an official inventory. While the ADF spokesman would not say what the stocktake had found, The Sunday Age believes most army weapons are now accounted for.

An audit of the police armoury had not begun, as the ADF had not received a full official inventory, the spokesman said. But The Sunday Age has obtained a detailed breakdown of that inventory. Before last month's crisis in which the police command disintegrated, the 3000-strong force had: 3500 Glock pistols; 88 FNC assault rifles; 180 Steyr assault rifles; 200 Heckler and Koch assault rifles; about 20 F2000 submachine-guns; and about 40 shotguns. The ADF spokesman would not comment on reports that at least half that armoury was missing.

The commander of Australian forces in East Timor, Brigadier Mick Slater, concedes some weapons will never be recovered. "There are so many weapons in this country," he told reporters on Friday. "I don't think that in my lifetime we will get all of the guns handed in. There will be guns hidden in the hills for many, many years to come."

Tracing army weapons was relatively easy. While army guns were given to civilians at the height of the security crisis, this was done in a controlled manner and most had been returned. The army also had detailed documentation on its armoury.

Tracing police weapons is more difficult. There is no single inventory and firearms had been given to groups of civilians over a longer time by Mr Lobato in a tactic to intimidate opponents and create a counter-force to the army, which remains loyal to President Xanana Gusmao.

"There have been credible reports that a number of (police) weapons have gone missing in recent times and before that," said Bob Lowry, a former Australian army officer and former national security adviser to East Timor's Government.

"There's no doubt that Lobato has been behind that. He's the guy that ordered them and they've been imported and allegedly many of them have disappeared."

East Timor's Foreign and Defence Minister, Jose Ramos Horta, said police weapons – not the army – remained the real security challengenge. He told the Jakarta Post that army command remained intact, despite divisions in the ranks. The police, on the other hand, had been "very factionalised with too many weapons", Mr Ramos Horta said.

Despite the gradual restoration of order in Dili, the weapons issue was causing fear among internally displaced people (IDPs), human rights activist Aniceto das Neves said.

"This is the issue in Dili and in the districts. People in government, in the ruling party, were delivering weapons to Fretilin members," he said. "Rumours about civilians getting guns make the people very afraid."

An informed source who asked not to be identified said the security crisis and political impasse would not be resolved until people were given the facts about weapons.

"It's all about the weapons. If you want to know the truth about the so-called death squads (allegedly set up by Mr Lobato), you need to trace the weapons," the source said.

"The IDPs aren't stupid. They're not moving until they know where the guns are. And the impasse between the politicians, it's largely tied up with who did what, with what weapons. My suspicion is we're not being told any facts, because on the police side the facts may be unhappy."

B& East Timor's two most revered leaders left yesterday for a quick summit on its security crisis with giant neighbour Indonesia. President Gusmao and Foreign Minister Ramos Horta flew to Bali for a meeting with Indonesian President Susilo Bambang Yudhoyono. They are due back today.