The Qatari head of a prominent Geneva-based human rights group has resigned after being designated by the US government as an al-Qaeda “terrorist financier and facilitator”.

Abd al-Rahman al-Nuaymi, president of Alkarama, which has worked closely with international advocacy groups, and Abd al-Wahhab al-Humayqani, a Yemeni rights activist, were made subject to sanctions on Wednesday by the US Treasury for allegedly supporting al-Qaeda affiliates in Syria, Iraq, Somalia and Yemen.

Washington’s “terrorist” designation of a senior rights activist with ties to Islamist movements comes as political Islam faces an assault from several western allies across the region.

The move also poses uncomfortable questions for human rights groups who have worked closely with Alkarama, a group they say has helped to provide credible information on abuses.

The US said Mr Nuaymi, a professor at Qatar University, has been supporting al-Qaeda for more than a decade and “was considered among the most prominent Qatar-based supporters of Iraqi Sunni extremists”.

The Treasury said Mr Humayqani, 41, reportedly assisted al-Qaeda in “gaining a foothold and safe haven” in Yemen.

Mr Nuaymi, contacted in Istanbul, denied the charges but declined to comment further immediately.

Alkarama’s executive director, Mourad Dhina, said Mr Nuaymi insisted the claims were politically motivated and called on Washington to provide proof.

Mr Nuaymi, who is now considering legal action, is a longstanding opponent of US policy in the region, added Mr Dhina.

“He has decided to resign from the foundation to avoid any misinterpretation,” Mr Dhina told the Financial Times. “We appreciate his move, which shows responsibility.”

Alkarama said it had not spoken to Mr Humayqani – who used to file reports on rights abuses to Alkarama – because he has no formal role with the group.

The FT was unable to reach Mr Humayqani for comment.

Alkarama was founded in 2004 and has been advocating on human rights amid the regional unrest of the Arab spring. The group has also documented civilian loss of life from US drone strikes in Yemen.

Gulf officials have privately voiced concerns about the group’s potential links to individuals espousing Islamist extremist ideas and agendas, while the group has been critical of many Gulf governments.

“We know Alkarama is not appreciated by the United Arab Emirates, Saudi Arabia and the new regime in Egypt,” said Mr Dhina. “We fear some misinformation has been sent over to the US.”

The terrorist designation could have diplomatic ramifications through the Gulf, given the allegations made against Mr Nuaymi, a national of Qatar, which is a US ally. Doha has over the past few years been promoting Islamist groups in the revolutionary struggles through the region, from Libya and Syria to Egypt.

But the United Arab Emirates and Saudi Arabia backed the military ouster of Egypt’s president, Mohamed Morsi, who had been supported by Doha.

Under Qatar’s new emir, who assumed the throne in June, the Gulf state is assuming a more co-operative regional stance, analysts say.

The US Treasury on Wednesday claimed Mr Nuaymi had this year ordered the transfer of nearly $600,000 to al-Qaeda via its representative in Syria.

Mr Nuaymi reportedly oversaw the transfer of more than $2m a month to al-Qaeda in Iraq for a period of time, while also financing al-Shabaab, a Somali extremist group, in 2012 and channelling funds to Yemen, the Treasury said.

Alkarama has worked with the UN and independent human rights groups, such as Human Rights Watch and Amnesty International.

Human Rights Watch declined to comment. But one official said the advocacy group had not worked directly with Mr Nuaymi.

Amnesty International said: “Alkarama has helped facilitate access to information on a number of cases of individuals who had been subjected to human rights violations such as arbitrary detention, torture and other ill-treatment, enforced disappearances and unlawful killings, including in Qatar.

“Amnesty International has seen the US authorities’ most recent statements regarding the financing of terrorism, but is unable to confirm their accuracy or otherwise.”

One human rights official says Alkarama, thanks to its close contacts in Islamist groups, has managed to get into zones of conflict earlier than multilateral organisations and produces solid documentation.

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