Delays in rebates to business taxpayers are mainly the result of extra security and not the fault of the systems, claims HM Revenue & Customs.
The comments come after a recent slew of criticism from accountants over delays in refunds for their clients.
An HMRC spokesman said: 'Some delays are a result of security checks. We have a duty to make sure it's doubly right.'
Ken Frost, accountant and fierce critic of HMRC, said: 'I understand that in some departments, customer waiting time has risen from three days to approximately eight weeks.'
This is despite the fact that, according to HMRC's 2008/09 accounts, it spent £64.4m on outside consultants, including logistics group Unipart.
The department has adopted motor industry methods for its PaceSetter programme to improve the processing of tax returns.
The slowness of tax rebates has also been attacked by the ICPA, a group representing smaller practitioners.Its chairman, Tony Margaritelli said: 'Delays in handing out refunds - valuable cashflow for many struggling firms - are so bad that HMRC has been forced to publish an apology to accountants and their clients as part of its regular guidance.'
And a firm of chartered accountants, Swansea-based HW Vaughan, successfully billed HMRC for £500 after it took seven months to sort out a £15,000 refund for a struggling client.
Partner Russell Halliday said: 'We kept being passed around departments, everyone was blaming everyone else and some paperwork had to be sent three times - there's simply no excuse for that kind of delay.'
He added: 'This was one of the worst cases I've come across with HMRC... they seem to be really struggling.'