Jeh Johnson told a congressional committee that two unnamed members of the Kurdistan Workers Party were set free by a U.S. immigration judge, fled to Canada, and are now seeking asylum there.
He said he was disappointed the men were allowed out of custody in the U.S.
"Not my preference," Johnson said of a judge's decision to free them. "They were released by the judge, and they fled to Canada and they are seeking asylum in Canada."
The Kurdish militant group, also known as the PKK, remains listed as a terrorist entity in both the U.S. and Canada — which placed it on the list in 2002 because of its association with bombings and kidnappings in pursuit of Kurdish independence.
But there's been a drastic reversal since 2002 involving the group: it's now aligned with the West in the fight against militants with the Islamic State of Iraq and the Levant.
The case of the two men is noteworthy for the political waves it made in the U.S. a few months ago.
The men were detained after attempting to enter the U.S. from Mexico — which fuelled right-wing warnings of terrorists sneaking into America from the south.
Johnson had attempted to douse those fears in October, when he announced that the detained men were not actually ISIL members and were in fact Kurdish opponents of Islamist militants.
On Tuesday, the issue came up during a congressional hearing on immigration, where Republicans attacked Johnson for the Obama administration's move to provide work permits to millions of illegal immigrants.
At one point Johnson was asked about those four Kurdish men who'd been detained while crossing the Mexican border. He announced, with regret, that two of them were gone.
"Two are detained. The two others were released by the judge," Johnson said.
Lawmaker Jason Chaffetz pressed him on the case. He asked whether Johnson would demand that they be brought back to the U.S. Johnson said he doesn't generally intervene in immigration cases.
That prompted a scolding from the California Republican lawmaker. He accused Johnson of flip-flopping from his previous statements, in his last appearance before the committee.
"You told the world that you were going to deport these four people with ties to a terrorist organization. That's not what happened," Chaffetz said.
"Two of them were released.... Doesn't that beg a lot of questions about what you're doing in deporting criminals? These people have terrorist ties."
The men are now in custody in Canada, with their claims pending.
Late Tuesday, the Canadian government issued a statement saying that anyone deemed to have been involved in serious acts, like war crimes and terrorism, would be excluded from Canada's refugee process.