Most of the world knows Abdul Rahman Omeir al-Naimi as a Qatari history professor and human-rights activist. The Swiss-based organization he founded, known as al-Karama from the Arab word for dignity, has worked closely with the United Nations and American human rights groups, most notably Human Rights Watch.

According to the U.S. government, however, al-Naimi is also a major financier of al Qaeda. On Wednesday, the Treasury Department issued a designation of al-Naimi that said he oversaw the transfer of hundreds of thousands of dollars to al Qaeda and its affiliates in Iraq, Somalia, Syria, and Yemen over the last 11 years. In 2013, the designation says, al-Naimi ordered the transfer of nearly $600,000 to al Qaeda via the group’s representative in Syria. In the same notice, the Treasury Department also designated Abdulwahab Al-Humayqani, al-Karama’s representative in Yemen, as a financier and member of al Qaeda in the Arabian Peninsula, the group’s Yemen affiliate. On Twitter, al-Naimi acknowledged that he and al-Humayqani, whom he calls by his first name, were designated for supporting terrorism. Al-Naimi has resigned as president of al-Karama’s board, but told the group’s senior leadership that he intends to challenge the Treasury Department’s designation.

If the Treasury Department’s allegations are correct, the story of al-Naimi, who until Thursday was the president of al-Karama’s board, illustrates how sometimes human-rights advocacy can also be used as political cover for jihadist networks. Al-Karama has advocated for the release of Hassan al-Diqqi, the leader of a banned political party in the United Arab Emirates. In 2010, the group claimed credit for forcing the U.N. Working Group on Arbitrary Detentions to criticize the Emirates for his detention. In September, however, the Washington Post reported that al-Diqqi appeared in a video earlier this year at a training camp for jihadist rebels in Syria.

While the Treasury Department did not single out al-Karama in its designation this week, U.S. allies in the Middle East have accused al-Naimi in the past of being a terrorist. Saudi Arabia has banned al-Naimi from entering that country, for example, the foundation’s executive director, Mourad Dhina, said in an interview.

Al-Naimi’s organization has in the past worked closely with the Center for Constitutional Rights (CCR) as well as the U.N. Human Rights Council. Al-Karama has also issued joint communiqués with Human Rights Watch, which specializes in legal advocacy on behalf of Islamist prisoners throughout the Middle East.

In April of this year, a staff attorney for CCR gave testimony before the Senate based in part on field research from al-Karama on the impact of the U.S. drone war in Yemen. Human Rights Watch has joined forces with al-Karama in campaigns to free political prisoners in the United Arab Emirates, Egypt, and Saudi Arabia

In an interview Thursday, Mourad Dhina, the executive director of al-Karama, said the news about his group’s founder and the head of its board came as a shock. “This is not good news for us,” he said.

Dhina said he had spoken Thursday with al-Naimi, who said he planned to resign as president of al-Karama’s board. But Dhina also said al-Naimi would challenge what he regarded as false charges against him. Al-Naimi also expressed this view on Twitter “He labels these charges as being purely politically motivated, owing towards his stance towards U.S. foreign policy,” Dhina said.

Dhina in the interview said no one had suspected al-Naimi of being connected to al Qaeda and stressed that al-Naimi did not play much of a role in the day-to-day activities for the group. Sarah Leah Whitson, executive director of the Middle East and North Africa division of Human Rights Watch, in an email acknowledged her group’s work with al-Karama, but she also said to her knowledge the group had no interactions with al-Naimi. “We believe the organization to be reputable, and we have had good interactions with their staff on a number of projects in the region,” she said. A spokeswoman for the CCR declined to comment.

But the signs were there for some observers that al-Naimi may be an extremist, particularly when it comes to women. A 2007 U.S. cable first disclosed by WikiLeaks described him as an “Islamist hardliner” who was “critical of women taking up public leadership positions.” On Thursday, Gulf News reported al-Naimi was arrested in 2009 for opposing co-education at Qatari universities.

“The NGO community is colonized by many people using human rights as a means to an end, not an end in itself,” said Thor Halvorssen, CEO of the Human Rights Foundation. “Usually it’s a cover to play politics, but it is appalling when it is used as a platform to neutralize the legitimate actions of governments fighting terrorism. The lack of due diligence regarding this organization by reputable groups in Europe and the United States is indicative of a deeper problem: choosing allies on the basis of agreeing with their conclusions as opposed to agreeing with their mission.”