Indonesian Foreign Minister Hasssan Wirayuda says the government will soon send its official response on the issue to U.N. Secretary-General Kofi Annan.
Foreign Ministry spokesman Marty Natalagawa says Jakarta does not agree with recommendations by the three-member UN Commission of Experts.
"Our position is absolutely clear," he said. "We find that the recommendations submitted have failed to meet the expectations which have been set, namely for the advisors' recommendations to be legally sound and also politically feasible."
Pro-Jakarta militias, many backed by the Indonesian military, went on a rampage before and after East Timor voted for independence from Indonesia in a U.N.-sponsored poll in 1999. About 2,000 people were killed.
Trials held by Indonesia ended last year with the acquittal of all but one of the 18 officers and officials accused of human rights violations in East Timor.
The three-member U.N. panel in its report called Indonesia's human rights court "manifestly inadequate" and said it showed little respect for international standards.
Mr. Marty says Indonesia and East Timor are striving for reconciliation through the Commission of Truth and Friendship set up by both countries.
"The Commission of Experts have failed to indicate its support for the Commission of Friendship, which the two countries have established as a way to promote a sense of closure to the issue and instead submit certain recommendations which to us are clearly not on," he said.
East Timor says it does not support an international tribunal and wants to establish good relations with Indonesia.
East Timor gained full independence in May 2002 after more than two years under U.N. supervision.