The Ibrox side could face court action over accusations that players were paid through offshore bank accounts.
The club are alleged to have begun making the payments over a decade ago through an employee remuneration trust.
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Hide AdThe cash-strapped club, who are in around 30 million of debt, could face a backdated tax bill running to millions of pounds.
Potential buyers of the club are unlikely to invest in the club until the issue is resolved.
Rangers said they would defend themselves "robustly."
A club spokesman said: "There is an ongoing query raised by HMRC, which is part of a pending court case.
"On the basis of expert tax advice provided to Rangers, the club is robustly defending the matters raised. It would, therefore, be inappropriate to comment further at this stage."
The cash-strapped Ibrox club, who won the Scottish Premier League on Sunday, has been placed up for sale by current owner David Murray.
Property developer Andrew Ellis and South African businessman Dave King have separately expressed an interest in taking over the club.
An HMRC spokeswoman said: "HMRC cannot comment on the confidential tax affairs of individuals or businesses."