Auditors Deloitte have raised concerns over an "uncertain outcome" of potential litigation, although Rangers have consistently said Whyte's claims are of no merit.
The "emphasis of matter" note is contained in the first annual report of Rangers International Football Club plc (RIFC), which revealed operating losses of £14 million.
RIFC has spent £600,000 contesting the claim by Whyte and associate, Aiden Earley, who have argued that former chief executive Charles Green was working alongside them in Sevco 5088, the company granted permission to buy the oldco assets by administrators Duff & Phelps, and that they, consequently, are the rightful owners of the club.
"The ultimate outcome of this matter cannot presently be determined, and accordingly no adjustments have been made to these financial statements as a result of this matter," Deloitte said.
Fans already concerned over the financial viability of the club after it emerged RIFC holds just £11m in cash after raising £35m in finance, are concerned that Craig Whyte remains the "spectre hanging over us".
Whyte released documents appearing to bear Mr Green's signature, confirming Whyte and his associate, Adrian Earley, as directors of Sevco 5088.
Meanwhile, Rangers directors have been accused of being "hell-bent" on denying shareholders their right to vote on the composition of the board after the club dismissed a resolution to appoint four new members.
The Rangers board claimed an attempt to install Paul Murray, Malcolm Murray, Scott Murdoch and Alex Wilson, in a proposed vote at the club's annual general meeting on October 24, was "unlikely to be properly constituted under s338 of the Companies Act 2006".
However, the group seeking change insists it submitted its request in a "perfectly valid" manner.