Charities wishing to file Gift Aid claims must from this week use the HM Revenue & Customs online filing system or a new paper form.
HMRC introduced Charities Online in April. Since then, a transitional arrangement had been in place under which charities could make Gift Aid claims using the old paper forms or the new online system.
The old paper form, known as an R68i, is no longer being accepted from this week.
HMRC has introduced a new paper-based form for charities that are unable or do not wish to make online claims.
Larger charities will have to submit applications using their own software. At a meeting last month, an HMRC official said he was aware of seven large charities that were having trouble submitting applications.
In mid-September, HMRC reported that 30,000 charities had enrolled for the new system and said it hoped that 40,000 would enrol by the end of the transition period.
The Charity Tax Group, the umbrella body that lobbies for a better deal for charities on tax, said that it had received positive feedback from many charities about the new service, but some charities had also encountered problems.
"We are pleased to report that many people using the spreadsheet solution have given positive feedback, and for many charities this will be the preferred option," a statement released by the CTG said. "There has also been positive feedback from charities about the quicker repayment times using the new system."
The statement said that the CTG was aware that some charities planning to submit claims using their own software had still been unable to make the transition because they were waiting for their software suppliers to supply upgrades.
"HMRC has ruled out any general extension of the transition deadline but has stated that, if charities are facing problems in meeting the transition, it will consider these on a case-by-case basis," the CTG statement said.