The Joseph Rowntree Charitable Trust has said it stands by a decision to give more than £250,000 of funding over six years to Cage, a human rights organisation whose outreach director, Moazzam Begg, was last week charged with terrorism offences.

Begg, a former Guantanamo Bay detainee who was held without charge for three years, was charged last week at Westminster magistrate's court with providing terrorist training and funding terrorism overseas, in connection with the conflict in Syria.

His organisation, Cage, was until recently was known as CagePrisoners. It describes itself as an “independent advocacy organisation” which campaigns against the war on terror. It has faced accusations of supporting the Taliban, including from Gita Saghal, former head of Amnesty International’s gender unit, who was suspended for her comments. It is not a registered charity.

Cage said in a statement last week that Begg has its full support. It called his arrest “politically motivated” and “an attempt to criminalise legitimate Muslim activity”.

Cage has previously received funding from mainstream charitable organisations including the JRCT, which made grants of £135,000 and £120,000 and the Roddick Foundation, set up by Body Shop founder Anita Roddick, which gave £120,000.

Both charities faced criticism for supporting the organisation in a Telegraph article published on Saturday.

Nick Perks, secretary of the Joseph Rowntree Charitable Trust (JRCT), said that his organisation continued to believe in Cage's work. He said that his organisation had looked closely at Cage’s work when it first allocated funding, and had decided that it did not support terrorism.

“We think what they’re doing is valuable,” he said. “There are still 155 detainees in Guantanamo, the vast majority of  whom have not been charged with a crime.”

However he said his organisation was concerned to hear of the charges and was “closely monitoring the situation”.

The Roddick Foundation could not be contacted for comment.