The ARU is currently locked in a messy battle with the Rebels and Perth-based Western Force after agreeing to cut one of the two teams as part of a competition revamp.
The Rebels' licence has been held by a private company, Imperium Sports Management, which is owned by businessman Andrew Cox. The ARU, however, said late on Friday it had heard via a third party that the licence had been transferred to the VRU and were seeking more information.
"The Melbourne Rebels have an obligation under their Participation Deed to inform ARU of any change of ownership," the ARU said in a statement.
"To date, ARU has received no such communication from the Melbourne Rebels despite recent attempts to confirm their position.
"ARU is urgently seeking to confirm the terms on which this transfer occurred."
Southern hemisphere rugby's governing body SANZAAR agreed earlier this year to reduce Super Rugby to 15 teams from next season against a backdrop of falling revenues and fan interest after the expansion to 18 sides last year.
Two South African sides, the Cheetahs and Southern Kings, have already departed and will join Europe's Pro-12 league, expanding that competition involving clubs from Ireland, Scotland, Wales and Italy to 14 teams.
(Reporting by Greg Stutchbury in Wellington; Editing by Peter Rutherford)
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