Rovers changed their mind about paying Berg his three-year contract in full, but judge Mark Pilling said at a High Court hearing that the manner in which the club filed the papers after the pre-agreed deadline was “woefully inadequate” and “entirely contrary to the way justice is supposed to be served”.
Berg - a former Rovers player - was dismissed as manager after just 56 days in charge in December.
He said: "I've come close to dismissing this application out of hand, but I'm just persuaded [to allow it]."
Rovers main owner Anuradha Desai has hired new solicitors who will argue at a later hearing that the club's managing director Derek Shaw had no remit to authorise Berg such a lucrative severance deal rather than the one-year pay she claims to have sanctioned.
The court, sitting in Manchester, said Shaw is subjected to disciplinary proceedings instigated by Desai for going against her order.
Desai's claim that Shaw had no authority is undermined by a press release on the Rovers website which claimed he had the "complete backing and support" of the owner.
"The owners' case was 'contradicted' by the website press release," he said.
Berg is still owed £1.6m from the club having been paid £562,000. The club will only avoid paying Berg the rest of the money if they can successfully argue that Berg and his agent should have known that it was the club's owners and not Shaw who made the final decision.
- Sports & Recreation