The status of around 6,000 local charities is likely to be void if they were registered before May 2019, a regulator has warned.
The admission follows a Court of Appeal ruling that decisions on charitable status made by a staff member at the Charity Commission for Northern Ireland (CCNI) - not a panel of commissioners - were unlawful.
The matter was raised yesterday on the Nolan Show, prompting concerns that charities may not have legal status.
However, the CCNI stressed that charities could "continue to operate as previously without any disruption to their operations".
The watchdog added: "Furthermore, the commission will be contacting as many charity funders and support bodies as possible in order to clarify the situation and request that this issue be taken into consideration when assessing applications from charities.
"A solution is being sought from the Department for Communities (DfC) in order to permanently resolve the issue regarding decisions.
"Further information and guidance will be provided on the commission's website."
The DfC assured the charities affected that they "remain charities in law and need do nothing differently in the interim".
It added that Caral Ni Chuilin, who is acting as Communities Minister in the absence of Deirdre Hargey, would shortly outline how the department intends to respond to the issues raised by the court judgment.
"The department is assured that the Charity Commission has introduced interim procedures to ensure decisions can be taken in compliance with the judgment," a spokesman said.