As much as £1.5bn in unpaid taxes could be written off by HMRC as a number of cases are more than two years old and could be open to legal challenge by taxpayers.
Front-line staff at HMRC told the BBC only those cases that verge on fraud will be pursued.
There is a backlog of more than seven million cases of tax underpayment or overpayment - the latter estimated at £3bn which will be reimbursed - dating back to 2007/8.
An HMRC spokesman said no decision had been made on underpayment cases.
The details come weeks after it emerged a further six million people had been wrongly taxed in the past two years, with 1.4m people who underpaid in line to receive an unexpected tax bill.
The latest cases to emerge are not on the HMRC's new computer system and will have to be dealt with manually.
Cases where money is owed to taxpayers by the Exchequer will still be processed.
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