Up to around 20,000 charitable organisations currently can't claim their Gift Aid payments after the introduction of a compulsory online system.
The government says more than 50,000 charities have signed up to Charities Online, which is designed to make it quicker and easier for charities and Community Amateur Sports Clubs (CASCs) to receive Gift Aid on their donations.
The government says the online system is much more efficient than the previous system of posting paper forms to HM Revenue and Customs (HMRC). This has reduced the time taken to process payments from 29 days to nine, it said.
Currently, over 50,000 organisations out of 70,000 that claim Gift Aid have registered online, and these charities have so far received over £380 million in Gift Aid repayments through Charities Online since the system was launched in April last year.
Charities Online has been the only option for claiming Gift Aid since October last year, which means, according to the government figures, up to around 20,000 currently can't claim it, unless they register with the site.
Nicky Morgan, economic secretary to the Treasury, said: "The government values the important work of charities in our society, and we want charities to maximise their donations. In 2013 charities and their donors received £4 billion in dedicated tax reliefs from the government.
"I am pleased that over 50,000 organisations have registered to use this service, which will speed up the rate that charities can access donations."
The government said the biggest claim made online so far by a single charity has been for £3.7 million. The busiest time for making claims was early September last year, when nearly 30,000 charities or CASCs visited the site in one week.