Former prosecutor says US was confident when charges were brought that the two men were part of a Hutu rebel group

The attorney who brought charges against two Rwandan men recently resettled in Australia says the United States was “certain” they were members of a Hutu rebel group that was later designated a terror group by the US government.

The comments again raise questions about how the pair managed to pass Australia’s tough and vigorously applied character and security checks, under which others have been deported for minor offences or historical associations with criminal groups.

The two men were members of the Army for the Liberation of Rwanda, an offshoot of armed militias responsible for the country’s 1994 genocide, and were accused of the targeted murder of western tourists in Uganda in 1999.

Resettlement of Rwandan rebels labelled a 'frustrating' hypocrisy Read more

They were brought to Australia in a secret deal with the US last year, and Scott Morrison has said they were assessed and cleared by security agencies. The prime minister said the agencies had assessed the specific allegations against the pair and they were “not found to be upheld in their view, and as a result they were allowed to come to Australia”.

But the federal prosecutor responsible for extraditing and bringing charges against the men said the US government had been confident in the evidence.

“I don’t have any comment on Mr Morrison’s claims,” Roscoe Howard Jr told Guardian Australia. “However, at the time, the United States was certain the crime against a US citizen was committed, and was certain the two gentlemen were part of a group that committed the crime.

“They were originally extradited to the United States to stand trial because of the confidence that we had in the evidence and our ability to show at a trial beyond a reasonable doubt their guilt.”

Howard stressed he was not speaking on behalf of the current District of Columbia attorney, who could not be reached by Guardian Australia before publication. He also said the proceedings had been more than a decade ago and he was not the prosecuting assistant, who would have better firsthand knowledge of the case.

The US trial against the pair collapsed after a court found they had been subjected to prolonged and disturbing torture by Rwandan forces before they gave shifting, inconsistent confessions. The pair could not be returned to Rwanda because of a reasonable fear of persecution, but were not granted asylum in the US, leaving them languishing in detention limbo.

Australia took them as part of its deal with the US and they were processed by Australian authorities between April and July last year.

In a much-publicised 2016 call between Malcolm Turnbull and Donald Trump, the former prime minister pledged to help the US with problematic cases. Turnbull told the president that Australia would take people that the previous Obama administration “were very keen on getting out of the United States”.

“We will take more,” he said. “We will take anyone that you want us to take.”

The decision to accept the two men appears to be at odds with the government’s otherwise hard line on assessments of character. The “character test” allows it to reject or cancel visas if it reasonably suspects applicants have had links to criminal groups.

The character test has been used with increasing vigour since 2014, when powers were broadened. The government can choose not to use the character test, and can approve visas if it believes this to be in the national interest.

New Zealand citizens who have lived in Australia long term have been deported for minor historical offences or old links to criminal groups.

The Rwandan pair – Gregoire Nyaminani and Leonidas Bimenyimana – were both found to be members of the Army for the Liberation of Rwanda in the US courts.

Court documents show they joined it after witnessing or being victim to horrific acts of violence. Nyaminani reached the rank of first sergeant, according to the documents, and Bimenyimana was a second lieutenant.

They were captured by Rwandan government forces during battles in 2001 and 2002.

One survivor of the 1999 attack in Uganda has cast doubt on whether the pair were actually directly responsible for the murders.

Elizabeth Garland, a US researcher, said the sheer number of those involved in the attack – between 100 and 150 – made her suspicious that those who committed the murders had actually been captured.

“It seemed very improbable that they would have caught the men that did the killing of the American victims, given the number of people involved in the attack,” she told the ABC.

Morrison was approached for comment.