Suharto's body was then flown on board an Indonesian air force jet to his hometown of Solo in central Java, where the funeral will be led by Susilo Bambang Yudhoyono, the Indonesian president.
Announcing Suharto's death on Sunday Yudhoyono declared a week of national mourning.
"I invite all the people of Indonesia to pray that may the deceased's good deeds and dedication to the nation be accepted by Allah the almighty," he said in a televised address.
"Suharto has done a great service to the nation."
Agung Laksono, the speaker of the Indonesian House of Representatives, called on
Indonesians "to pray so that the soul of the late [Suharto] be accepted by God almighty, that his sins be pardoned and his good deeds be received."
Several current and former regional leaders including Mahathir Mohammad, the former Malaysian prime minister, are expected to attend Monday's funeral.
Also attending will be Xanana Gusmao, the prime minister of East Timor and the former head of the guerilla resistance to Indonesian rule over the now independent country.
Suharto will be buried in his family's mausoleum on the outskirts of Solo next to the tomb of his wife who died in 1996.
The former president's admission to hospital in critical condition earlier this month sparked a national debate over his legacy.
Suharto was forced to stand down in 1998 amid widespread protests triggered by the impact of the Asian financial crisis.
He was accused of siphoning off billions of dollars in state funds into his own secret bank accounts, but his lawyers successfully argued that he was too ill to stand trial.
|Suharto's eldest daughter called for |
forgiveness for her father's "faults" [AFP]
According to one study, by corruption watchdog Transparency International, Suharto and his family embezzled up to $35bn during his 32 years in power.
He was also accused of presiding over some of the bloodiest episodes in post-second world war Asia, including the crushing of the Indonesian communist party in the mid-1960s, and the invasion and occupation of East Timor a decade later.
Both incidents led to the deaths of hundreds of thousands of people.
Speaking shortly after his death on Sunday, Suharto's eldest daughter, Siti Hariyanti "Tutut" Rukama, called for forgiveness for her father.
"Father has returned to God," she said, speaking outside the central Jakarta hospital where he had been treated for the past three weeks.
"We ask that if he had any faults, please forgive them ... may he be absolved of all his mistakes."