The First and Deputy First ministers have urged community leaders to make a clear choice between paramilitarism and legitimate work.
It comes after the Assistant Chief Constable admitted there were elements of the UDA working with a government supported group in East Belfast.
Stephen Martin said individuals connected to Charter NI are engaged in recent paramilitary activity.
The organisation was a benefactor of the executives 'Social investment fund' and is headed by Dee Stitt.
Charter NI says the Police Chief's comments came as a surprise and that it was seeking an urgent meeting with officers.
It said it did not condone illegal or criminal activity of any kind.
A spokesperson for The Executive Office said: “This is not an insignificant comment by Assistant Chief Constable Martin. We will be in contact with the PSNI to seek further clarification.
“Where there is evidence of criminal activity, we expect the police to investigate and bring those responsible before the courts. Courts and jail are the only place for anyone involved in paramilitarism.
“There can be no acceptance of or ambivalence towards illegal activity.”
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