The Charities Commission is reviewing its procedures after a court ruled that its registration process was unlawful.
The Court of Appeal decision applies to some 6,000 charities registered prior to May 2019.
The commission said the organisations remain charities in law and can continue to operate as normal.
Communities Minister Carál Ní Chuilín is now weighing up the potential impacts of the judgment.
A spokesperson said she would want to ensure future arrangements were "in the wider public interest".
The court ruling, issued in February, said all commission decisions must be made by the board of commissioners, or a committee with delegated authority, rather than by commission staff.
'Decisions now void'
In a statement on its website, the commission said: "Up until May 2019, the vast majority of decisions relating to whether or not an organisation should be registered as a charity were made by the commission's registration team.
"This was in keeping with the processes agreed by the board of commissioners based on an interpretation of the law at that time.
"The Court of Appeal judgment has clarified the position and means those decisions are now considered to be void as they were not made at commissioner level."
It added that while some commission decisions may be delayed and the volume of decisions being made had been reduced, work on applications, requests and queries was ongoing.
Seamus McAleavey, of the Northern Ireland Council for Voluntary Action (Nicva), said a lot of charities are likely to be very confused.
"A lot of charities will wonder if their status has completely changed," he said.
"I don't think that is the case, but I do accept that what the Charity Commission is saying is that we are all still charities in law just no longer registered."
He added: "Charities have done no wrong. What I expect is government will move now to fix this problem.
"We would expect this to be fixed and clarified for people."
A spokesperson for the Department for Communities said it accepted the Court of Appeal judgment, which "raises complex issues in respect to charity regulation in NI from 2013 when the Charity Commission began registration and going forward".
It added: "As such, the minister will want to understand all of the potential impacts of the judgment on past decisions to determine what is in the best interests of all stakeholders and to ensure that any future arrangements are fully considered as they will set the course for charity regulation in NI and must be in the wider public interest.
"The department is assured that the Charity Commission has introduced interim procedures to ensure decisions can be taken in compliance with the judgment.
"The minister will shortly determine how the department intends to respond to the issues raised by the judgment.
"In the meantime, the department can give an assurance to those charities that were unlawfully registered that they remain charities in law and need do nothing differently in the interim."