'Son of the nation'
"We have lost a son of the nation, the most excellent diplomat we ever had," Primo Alui Joelianto, a senior Indonesian foreign ministry official, said.
Dino Patti Djalal, a presidential spokesman, said that Yudhoyono was "sad and shocked" by the news of his death.
"I cannot spell out his achievements but in the milestones of his career, his highest achievement was when together with the French government he helped to solve the bloody conflict in Cambodia. But ironically he didn't get the credit he deserved from it," Djalal said.
The Indonesian embassy said Alatas's body would be flown from Singapore to Jakarta later on Thursday for a funeral service at his family home.
East Timor blot
For all his accomplishments, Alatas's career was stained by the turmoil following East Timor's vote for independence in 1999, when Indonesian militias killed about 1,000 East Timorese according to UN estimates.
Alatas' account of events there, titled The Pebble in the Shoe: The Diplomatic Struggle for East Timor, helped start a wider debate about the crisis among official circles.
Despite his skills as a diplomat, Alatas struggled to justify the brutal events in East Timor, Damien Kingsbury, an associate professor at Deakin University in Australia, said.
"No matter how much he tried, he was always going to be trying to justify an appalling situation to the international community," Kingsbury said.