The Charities Aid Foundation, operator of the Give As You Earn scheme, which has 70 per cent of the payroll giving market in the UK, replaced the unique reference numbers of all donors in a database upgrade.
The change meant that member charities couldn't track who was giving to them, whether donors had stopped giving, or if they had changed the level of their gift.
Karen England, director of Childlife, a fundraising consortium of four fundraising charities that has about 2,000 payroll givers, said she was "incredulous" about the change.
"It has caused a huge amount of disruption and cost to charities," she said. "We have had to pay for a temp to come and help us sort it out. CAF's attitude is a sorry replacement for decent consultation."
Payroll Giving Monitoring Services is advising its 30 charity clients to make a formal complaint to CAF about the change.
CAF promised Karen England that it would run the old reference numbers alongside the new ones in statements from June for another 12 months. Around 350,000 people donate £60m through Give As You Earn each year.
A CAF spokeswoman admitted to "a lack of insight on our part as to how charities use these numbers".