The United States said it was disappointed with the work of an Indonesian tribunal into atrocities in East Timor, after it jailed a convicted general for just three years – a sentence branded by activists here as "a joke."

The United States handed down its verdict despite the fact that, in jailing Major General Adam Damiri, the Jakarta tribunal had ignored an acquittal recommendation by prosecutors. Damiri was the last and most senior of 18 defendants to appear before the court over the Indonesian army-backed wave of bloody militia violence against East Timorese independence supporters in 1999.

"The United States is disappointed with the performance and record of the Indonesian ad hoc tribunal," said State Department deputy spokesman Philip Reeker. "We believe that the overall process of the tribunal has been flawed and lacked credibility," he said, though he added that US officials were pleased it did at least end with a conviction.

But he also pointed out that the three-year sentence did not meet the minimum term recommended under Indonesian law. "If you look at all of the cases of this ad hoc tribunal together, I think it's been a very disappointing process in terms of rendering justice onto those who've committed horrible atrocities in East Timor just a few years ago," said Reeker.

US-based East Timor activists ridiculed the three-year jail term. "The punishment does not fit the crime," said John Miller, spokesman for the East Timor Action Network. "Today's three-year sentence for General Damiri is a joke and has done nothing to boost the laughable credibility of Indonesia's court. The international community has been taken for a ride. The question is: what is it going to do about it?"

Damiri, a former regional commander responsible for security in East Timor while it was still Indonesian territory, branded the verdict as political, vowing to appeal. The judge in the case ruled that Damiri should have taken immediate corrective steps to address any violations by his subordinates.

Unlike US activists, Jakarta-based campaigners welcomed the verdict, after previously dismissing the Jakarta court as a sham. Indonesian Foundation of Legal Aid chairman Munarman said, "This is a rare verdict and this is definitively a milestone in the upholding of human rights here." He praised the judges as having shown "extraordinary courage".

Muhammad Asrun who heads Judicial Watch called the court's decision "very important". But he added that three years was not a long enough sentence "because he [Damiri] held the primary responsibility over security in East Timor".

The court was set up to deflect pressure for an international tribunal into the bloodshed but international and local rights groups have called it a sham. Eleven security force members and one civilian have been acquitted by the court. Five people – two army officers, a former Dili police chief, the former civilian governor and an ex-militia chief – were ordered jailed but remain free pending appeals.

Damiri has also been indicted by UN-funded prosecutors in East Timor for crimes against humanity.