Although the Treasury, which has now closed the loopholes, has not named the bank, the schemes were widely linked to Barclays.
The bank is reported to be in disagreement with the Treasury’s estimate of a £500m loss, saying the real figure is less than £200m.
It is the first time the coalition government has clawed back taxes which have been avoided in the past. It will also ensure that billions of pounds of tax are paid in the future.
Barclays flagged up the schemes to Revenue and Customs, but the government decided they were not suitable for a company that had signed up to the tax code of practice.
Tax avoidance
One of the tax schemes involved a bank avoiding corporation tax on profits it made buying back its own IOU-notes.
The other scheme, which is understood to have been devised by the same bank, involved investment funds trying to receive tax credits from the Treasury on non-taxable income.
On Monday, the government brought in legislation to block future use of the scheme.
Exchequer Secretary to the Treasury, David Gauke, said the government was clear that “business must pay the tax they owe when they owe it”.
He added: “The government wants to ensure that the tax system is fair for all and we will not allow those who seek to benefit from this aggressive avoidance to get an unfair advantage.
“We do not take today’s action lightly, but the potential tax loss from this scheme and the history of previous abuse in this area mean that this is a circumstance where the decision to change the law with full retrospective effect is justified.”