Six million people are to receive tax repayments averaging £400 this weekend, while another 1.2m will receive a bill for £600.
HMRC is sending letters to customers in the next few months over the discrepancies, which total more than £2.5bn in excess payments and date back to 2001.
The 1.2m people who have underpaid, include around 150,000 pensioners.
Last year, the HMRC identified 4.3m people who had overpaid on tax, while 1.4m had underpaid. The amount owed averaged £1,400, while 900,000 underpayments of up to £300 were written off.
A HMRC spokesman says: “Money that is owed going back many years is now going to be automatically paid back as we get the tax system up to scratch,”
“We are getting cases that were left unreconciled up to date as quickly as possible. Anyone owed money will be paid back with interest without the need to contact us.”