The 17 April elections were the first time the country of 260 million people combined the presidential vote with national and regional parliamentary polls, with the aim of cutting costs.
Voting was largely peaceful and was estimated to have drawn 80 per cent of the total 193 million voters, who each had to punch up to five ballot papers at one of more than 800,000 polling stations.
But conducting the eight-hour vote in the archipelago that stretches more than 5000 kilometres from its western to eastern tips proved to be both a Herculean logistical feat and deadly for officials, who had to count ballot papers by hand.
As of Saturday night, 272 election officials had died, mostly from overwork-related illnesses, while 1878 others had fallen ill, Arief Priyo Susanto, spokesperson of the General Elections Commission (KPU), said.
The Health Ministry issued a circular letter on Tuesday urging health facilities to care for sick election staff, and the Finance Ministry is working on compensation for families of those who had died, Mr Susanto added.
The KPU has come under fire due to the rising death toll.
"The KPU is not prudent in managing the workload of staff," said Ahmad Muzani, deputy chairman of the campaign of opposition presidential candidate Prabowo Subianto, reported by news website Kumparan.com.
Mr Prabowo, who independent pollsters said was the loser of the 2019 polls, had alleged widespread cheating and his campaign claimed some officials punched ballots in favour of incumbent President Joko Widodo. Mr Widodo's security minister said the allegations were baseless.
Both candidates have declared victory, though quick counts suggested Mr Widodo won the election by around 9-10 percentage points.
The KPU will conclude vote counting and announce winners of the presidential and parliamentary elections on 22 May.