Last month oldco Rangers won its appeal in principle against a bill from HMRC over its use of Employment Benefit Trusts (EBTs) from 2001 to 2010.
The tribunal stated that the "controversial monies received by the employees were not paid to them as their absolute entitlement".
Today a spokesman for HMRC said it is appealing against the decision.
"HMRC will seek permission to appeal the tribunal decision."
Rangers argued that the payments, thought to be close to £49 million, were loans rather than wages and not subject to tax.
The oldco was consigned to liquidation in June after it failed to exit administration via a company voluntary arrangement.
Parties need to apply to the tribunal to seek leave to appeal and HMRC has started that process, the spokesman said.
A First Tier Tax Tribunal heard Rangers' appeal over the EBT bill over 29 days and last sat in January.
It delivered a majority verdict two weeks ago which allowed the appeal in principle and declared that the assessments of HMRC be "reduced substantially".
Two of the three judges decided that only some of the payments made to players through EBTs were taxable but that many of them could be described as loans, as the club had argued.
Rangers was under the control of Sir David Murray when it began using EBTs. He sold the club for £1 to Craig Whyte in 2011, while the tax liability was in dispute. The old club went into administration in February owing up to £134 million to unsecured creditors, including HMRC.
Whyte had stated that the tax liability could have been as high as £75 million, including interest and penalties, for payments made from 2001-10.
Although no final figure was revealed in the 145-page verdict, Murray International Holdings (MIH), the former majority shareholders of the liquidated club, declared themselves vindicated after being left with what they described as "minimal tax liability".
In a statement, two tribunal judges agreed with the club's outline case.
They stated: "The majority view reflects the argument that the controversial monies received by the employees were not paid to them as their absolute entitlement.
"Thus the payments are loans, not earnings."
The decision came too late to save oldco Rangers from being wound up and does not directly affect the current Ibrox regime.
Charles Green led a consortium which purchased the business and assets of Rangers after they were consigned to liquidation in the summer.
The Ibrox side was subsequently relaunched as a newco in the bottom tier of Scottish football.