A Quaker trust funded a charity which is under investigation by the Charity Commission for Northern Ireland.
It reported that CRSI’s offices have been raided by anti-terrorism police twice.
The PSNI said detectives had searched an office on Belfast’s Falls Road and seized a number of items in June.
The Joseph Rowntree Charitable Trust told the BBC it had “no relationship with armed groups or proscribed organisations”.
CRSI offers a mediation service for people threatened by paramilitary punishment attacks, and the Charity Commission said an inquiry was opened into the organisation in April 2017.
The BBC has contacted the CRSI for comment.
The Joseph Rowntree Charitable Trust said its “funding portfolio” included work with groups transitioning from violence in loyalist and republican communities.
Stating that it has worked to end violence in Northern Ireland, the trust also addressed a number of allegations made in the Times.
It said allegations made against four people associated with CRSI were “historic”.
It said three out of the four allegations related to periods before the individual concerned became associated with the charity.
In the fourth case, the individual’s employment with the charity was terminated after his arrest.
“During a two-year period leading up to their most recent grant, CRSI sought to mediate on behalf of 704 individuals who felt they were under threat of paramilitary violence,” the trust said.
“CRSI were able to successfully resolve almost all of these cases: protecting lives and reducing harm.
“CRSI have also made a significant contribution by their engagement with republicans who are outside the peace process.”
In July, it emerged the Charity Commission was investigating claims the JRCT gave £275,000 to a group linked to a banned terrorist organisation in Northern Ireland.
The funds were given to Teach Na Failte, which supports ex-prisoners but has links to the Irish National Liberation Army (INLA).
At the time, the watchdog said the charity needed to “explain and justify” its decision.
The JRCT said it had “no relationship with any proscribed organisations”.
The Charity Commission’s chief executive Frances McCandless said: “While we cannot comment on an open inquiry, we can make it clear that a charity’s trustees must act in the best interests of the charity and only within the purposes of the charity, regardless of any external affiliations.
“Charity trustees are also responsible for the reputation of the charity and should not act in a way which may bring the charity into disrepute.
“As our guidance highlights, where someone within or connected to the charity is found to have business with or links to terrorist groups, the commission expect this to be reported to us and the PSNI immediately, including how the issue is being managed.”