John Gittings in Jakarta and John Aglionby in Ambon – Indonesians flocked to the polls with enthusiasm yesterday for the country's first free elections in more than 40 years.

More than 90% of those eligible had registered to vote and turnout was high except in the strife-torn areas of Ambon, East Timor and Aceh.

Early returns for the parliamentary elections showed the expected surge in support from urban voters for the Indonesian Democratic Party of Struggle (PDI-P) led by Megawati Sukarnoputri, the daughter of the president ousted by Suharto in 1967.

Party officials were claiming 50% support in Jakarta and even more from outlying provinces. But electoral officials warn that reliable results will not be available for up to two days, as the votes of the rural predominantly Muslim population are counted.

Polling in Jakarta was a sociable affair in which communities gathered to vote and then to watch each ballot paper counted before their eyes.

Many began queueing before 8am as officials struggled to master the procedure for a contest between 48 different political parties.

Two years ago, in the election stage managed by the former president Suharto, there were only three parties.

"I'm number 112 on the list to vote," said one employee at the Tanjung Priok dockyard in Jakarta. "I'll probably have to wait till midday for my turn but I don't mind. We can see everything happening in front of us."

At Suharto's home polling station, Golkar – the government party which he created – was trounced into ninth position. But observers believe that the party may still win enough votes overall to influence the decision on who becomes president in November.

The mood in the growing number of trouble spots was less cheerful. Voting was postponed in three districts in Aceh while in East Timor turnout was extremely low.

In the town centre of Ambon, where the death toll from unrest has been greatest, people voted against a background of thousands of burnt out buildings. There also, Golkar support plummeted from the 85% share they received in 1997.

But when polling began at a station on Karang Panjang hill only eight people were waiting. Jon Ilela, a retired teacher, said: "People are keen to participate in the elections but they don't want to get caught up in a riot."

Some 13,000 soldiers are currently patrolling the island to prevent more unrest. "Everyone is traumatised by what has happened," said Brigadier-General Max Tamaela, the regional commander.

But as the spectre of violence receded, polling stations became busier. Many were full when they were supposed to have closed and dozens stayed to watch the count.

"We've been under the thumb of the Golkar for three decades," said one pedicab driver. "I want to make sure that they don't manipulate this election as well."

Golkar is blamed for the current chaos in Indonesia, but a future government will need to tackle it fast, according to Mynrik Batlolona of the University of Pattimura in Ambon.

"There are so many issues; Muslim versus Christian, local versus migrant," he said. "If the new government does not sort out the relationship between the capital and the provinces quickly, I reckon the troops will be on the streets for a long time to come."

On Ambon, where religious differences have led to violence, the voting also split on sectarian lines, with Christian areas flocking to Megawati's party while Muslims backed the Suharto-era United Development Party.

"There has not been enough time for the new parties to establish a footing in as remote a place as this," the provincial governor, Saleh Latuconsina, said.

Elsewhere the day passed peacefully and the police presence was generally low-key – though reserves were deployed out of sight in potentially troublesome areas.

Most polling was done under makeshift tarpaulin shelters, in voting booths knocked together from plywood and draped with a white cloth for privacy.

Teams of witnesses and monitors watched until the polls closed in smaller precincts. At polling stations in Jakarta, every vote for Megawati was cheered while the smaller numbers for Golkar was greeted with mock amazement.

There were claims that Golkar had handed out money and food over the weekend in a last-ditch effort to buy votes. Some voters said that they would "take the money and still vote for Megawati".

The former president, Suharto, was shown on Indonesian television voting in an election which he would never have tolerated while in power. He even pronounced that it should become "the basis for democratic life".

International observers said that in spite of hitches the election had been generally fair. "It is almost like a ceremony. The question is whether the hopes will be fulfilled," one European Union monitor said. "There has been plenty of misfeasance but practically no malfeasance," said another observer.