Electoral officials had planned to announce the final results, but 27 out of 48 parties failed to sign off, saying the election was unfair.
They have cited nearly 100,000 irregularities, which must now be addressed by an electoral watchdog body. Senior officials are split over whether the complaints are justified.
The election was the first free ballot in Indonesia in 44 years. The result, already delayed by painfully slow procedures as well as bureaucratic bungling and bickering, is regarded as crucial to the democratic transformation of the world's fourth-most populous nation after decades of authoritarian rule.
Monday's delay has thrown Indonesia's electoral process into disarray. It could postpone the formation of the new parliament as well as an electoral college that is scheduled to pick the next president.
The final figures are expected to closely mirror previously released unofficial tallies that gave Megawati Sukarnoputri's Indonesian Democratic Party of Struggle a clear lead with 34 percent of the vote. The ruling Golkar Party, which underpinned the 32-year autocratic rule of ex-President Suharto and now backs his handpicked successor, President B.J. Habibie, came in second with 22 percent.
A two-thirds majority of the 53-member General Election Commission must endorse the final results.
The commission's head, retired Gen. Rudini, later met with Habibie in an attempt to break the deadlock. Rudini, like many Indonesians, uses one name.
Habibie referred the matter to Indonesian Supervisory Electoral Committee, which has one week to rule whether the allegations of irregularities hold any substance.
All five major parties, which won 93 percent of the 105 million votes cast, endorsed the result as fair, Rudini said.
Rudini was among those who refused to sign in his capacity as a representative of a small party. "They have justified reasons especially on [whether it was a] just and honest election," he said after his meeting with Habibie.
Other electoral officials disagreed.
Indria Samego, an analyst at the Indonesian Institute of Science accused small party leaders of trying to derail the electoral process. "They will lose face in defeat. So they are now trying to sabotage the election," he said.
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