HM Revenue & Customs has written to charities yet to sign up to its new online Gift Aid system to remind them that the old paper claim forms will not be accepted from the end of September.
The letters, sent on Monday, say that HMRC will stop accepting the old forms from 30 September and charities must make all Gift Aid claims using the new system, Charities Online, from 1 October.
Since it went live on 22 April, more than 19,000 charities have signed up to Charities Online and almost 50 per cent of Gift Aid payments are being made through the new system, HMRC said.
An HMRC spokesman said: "We expect only very few charities will be unable to meet the 30 September deadline.
"We are making individual arrangements with charities that have told us they cannot meet the deadline because they cannot update their IT systems in time."
The letter says that charities will need to allow up to 15 working days from the day they sign up before making their first claim.
Charities with no access to the internet can claim using a new type of paper form, called a ChR1. These can be ordered from the Charities Helpline on 0845 302 0203.