Jakarta will "continue trying to thaw" relations with Washington through dialogue, Sudarsono said, admitting he faced a tough job due to Indonesia's failure to meet international demands for heavy sentences for officers guilty of rights abuses.
Last week outgoing US ambassador for Indonesia Ralph Boyce said Jakarta had "missed its opportunity" to restore military ties by failing to make its soldiers accountable for abuses in East Timor.
United States officials have repeatedly expressed their disappointment at the outcome of tribunals set up to try military, police and civilian officials accused of atrocities linked to East Timor's violent separation from Indonesia.
In August, the Indonesian supreme court overturned the convictions of four Indonesian security officers, meaning that no members of the security forces were found guilty of rights abuses in East Timor.
Only two of 18 original defendants stand convicted, and both are East Timorese civilians.
Sudarsono, who headed the same ministry in 1999, said he wanted talks with the US Congress, the department of defense and rights watchdogs to "explain situations and conditions in the field" faced by Indonesian soldiers.
"We can't just condemn them as gross human rights violators," said Sudarsono.
Deputy spokesman of the US State Department Adam Ereli has said the Indonesian tribunal process "was seriously flawed and lacked credibility."
Military cooperation with the United States was sharply reduced in 1999 when Congress in Washington passed the so-called Leahy Amendment during the East Timor turmoil.
Under the amendment, assistance is suspended until certain conditions are met, including effective measures to bring to justice members of the armed forces and militia groups suspected of rights abuses.
The United Nations alleges that the Indonesian military and its militia proxies murdered at least 1,400 people during the August 1999 independence vote.
Restoration of military equipment assistance depends on accountability over the East Timor abuses while funds for military education have hinged on another case, the ambush killing of two Americans in Papua province two years ago.
Indonesia expressed hope in June that the Papua case was no longer an obstacle after the United States decided to blame Anthonius Wamang, a Papuan separatist rebel, with the killings.