General Endriartono Sutarto was responding to the 2000-page, internationally funded Reception, Truth and Reconciliation Commission report, which was handed to Kofi Annan, the UN secretary-general, by Xanana Gusmao, the president of East Timor, on Friday.
The report, compiled over two years, has concluded that the policies of the Indonesian military against East Timor's civilian population caused the deaths of 84,000 to 183,000 people - up to a third of the territory's population - during Indonesia's rule from 1975 to 1999.
Speaking on local radio, General Sutarto said: "I am not at all sure whether such a huge number of deaths came about as a result of the actions of Indonesia's armed forces and police at that time."
He also denied the report's claim that troops used napalm against East Timorese civilians.
Badly kept secret
"It is not true that we deliberately carried out massacres using napalm and starving people. That is not true at all," he said. He said that the military keeps data that will exonerate the actions of the Indonesian security personnel.
The report has not been publicly released, but excerpts were leaked and published in The Australian newspaper.
The report says that 90% of deaths were caused by starvation.
Indonesia and East Timor have repeatedly said they do not want to open old wounds and have rejected recommendations made in the 2500-page report.
"It is not true that we deliberately carried out massacres using napalm"
General Endriartono Sutarto
Indonesia invaded the former Portuguese colony of East Timor in 1975, largely unopposed by the international community.
But after 24 years of rule, international observers had grown increasingly crtitcal of Jakarta's behaviour in the territory and led to a vote for independence.