The regulator issued a statement on Monday confirming that it had operational compliance cases open into the two charities over their funding of Cage, which is not a charity, after Cage appeared to say that the UK security services played a part in radicalising the terrorist known as "Jihadi John".
Asim Qureshi, research director of Cage, said during a press conference last week that Mohammed Emwazi, a graduate of the University of Westminster who has been named as the Islamic State executioner, was "a beautiful young man" and harassment by MI5 and other anti-Islamic forces had contributed to his radicalisation.
In a statement published on Friday evening, the commission said that since the Cage press conference, the regulator had asked the two charities for urgent assurances that they had ceased funding Cage and would no longer do so, because of concern that such funding could damage public trust and confidence in charity.
The JRCT said that it had been subject to "intense regulatory pressure" to guarantee that it would no longer fund Cage. It awarded grants to Cage totalling £305,000 between 2007 and 2014, handing over a total of £271,250. The Roddick Foundation provided £120,000 of funding to Cage between 2009 and 2012.
"Last week, public statements by Cage officials heightened concerns about the use of charitable funds to support their activities," the commission’s statement said.
"In our view, those statements increased the threat to public trust and confidence in charity and raised clear questions for a charity considering funding Cage’s activities as to how the trustees of those charities could comply with their legal duties as charity trustees.
"In these circumstances, the commission took robust action and on 2 March required further unequivocal assurances from the two charities that they have ceased funding Cage and had no intention of doing so in the future."
The commission said that the Roddick Foundation provided assurances within 24 hours, but the JRCT did not provide an unequivocal assurance that it would not fund Cage in the future.
"Yesterday, the trust stated that this was an extremely difficult decision to make, but in the interests of all its grantees and the other work of the trust, the trustees confirmed that they have decided to give the commission an assurance that it will not fund Cage either now or in the future," the regulator’s statement said.
A spokesman for the JRCT said: "In the last week, we have been put under intense regulatory pressure to rule out any future funding of Cage regardless of any future changing circumstances.
"In the light of regulatory pressure, and to protect the interests of all our grantees and the other work of the trust, we have decided to publicly confirm that we will not fund Cage either now or in the future."
The commission said that it would shortly close its operational compliance cases on the two charities over their funding of Cage, which were both opened in December 2013.
The statement said that the commission expected all charities and trustees to ensure that all charitable funds were used in accordance with their charity’s purposes and in the way that the public would expect.