The April 17 elections were the first time the country of 260 million people combined the presidential vote with national and regional parliamentary ones, with an aim to cut costs.
Voting was largely peaceful and was estimated to have drawn 80 percent of the total 193 million voters, each of whom had to punch up to five ballot papers in more than 800,000 polling stations.
As of Saturday night, 272 election officials had died, mostly from overwork-related illnesses, while 1,878 others had fallen ill, Arief Priyo Susanto, spokesman of the General Elections Commission (KPU), told Reuters news agency on Sunday.
The health ministry issued a circular letter on April 23 urging health facilities to offer the utmost care to sick election staff, while the finance ministry is working on compensation for families of the deceased, Susanto added.
The KPU has come under fire because of the rising vote-count 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.
Prabowo, who independent pollsters said had lost the 2019 polls based on quick counts, has alleged widespread cheating and his campaign claimed some officials punched ballots in favour of incumbent President Joko Widodo.
Widodo's security minister said the allegations were baseless.
Both candidates have declared victory, though quick counts suggested Widodo won the election by about 9-10 percentage points.
The KPU will conclude vote counting and announce winners of the presidential and parliamentary elections on May 22.