The club had already extended their notice of intent once and had been hopeful they would be given a further 10 days at a hearing at Leeds County Court on Tuesday.
Rotherham said they owed the money to the Inland Revenue due to falling attendances as well a smaller than expected insurance claim for summer flood damage.
The club were saved from liquidation in 2006 when creditors agreed to a Company Voluntary Agreement.
They were also then hit with a 10-point penalty, which eventually cost them their League One status when they were relegated last season.
BBC Radio Sheffield understands chairman Dennis Coleman does not have the money to bankroll the club.
Despite spending much of the last month in negotiations to try and bring in further investment, Coleman has yet to find a backer.
The club have appointed XL Business Solutions as the administrator.
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