According to the Times, the regulator is investigating the claim that the trust gave the funds to Teach Na Failte, which supports prisoners and ex-offenders but was also founded by the Irish Republican Socialist Party - the political wing of the Irish National Liberation Army (INLA).
The Charity Commission on Friday ordered the York-based trust to "explain and justify" why it gave funding to a group whose offices were raided this year by anti-terrorism police investigating sex-trafficking, violent intimidation and "paramilitary-style attacks".
The INLA was formed in 1974 during the Northern Ireland conflict and has been linked with bombings and shootings in Northern Ireland and London, including the killing of shadow Northern Ireland secretary Airey Neave in Westminster in 1979.
The Times reported that the Rowntree charity has been giving money to the unregistered charity Teach na Failte since 2014.
A spokesperson for the Rowntree trust told the newspaper it "rejected all violence" and supports "equality, rights and reconciliation". The spokesperson also defended providing funds to Teach na Failte because it was "committed to non-violence".
They went on to describe Teach na Failte as a "support group for prisoners and ex-prisoners" who were associated with the INLA, which declared the end of its armed campaign back in 2009.
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