Plans to move 1,500 jobs and five departments from London to Salford Quays could be delayed for up to a year, or worse, abandoned due to a lack of government cash.
The scheme, called MediaCity:UK, was due to be completed by 2010, but is now under threat due to a hold-up in the licence fee settlement.
BBC director general Mark Thompson said he may be unable to recommend the move to Salford at all if there was a low settlement.
He said: 'We would have to find other, more modest ways of increasing our investment in the North.'
The remarks have forced broadcasting minister Shaun Woodward - responsible for the fee decision - to hit back, describing the claims as a cynical move to put pressure on the government.
He said: 'Cynicism is unwise on the BBC's part when it comes to Salford. The public expects the BBC to be strong, independent and good value for money. But value for money means employment isn't restricted to London.'
The massive Salford development would create more than 700,000m 2of new retail, commercial and residential space on the waterfront site.
A licence fee announcement is expected by the end of the month. This will leave BBC governors little time to come up with a plan, as their positions are set to be abolished at the end of the year.
The decision over the move will then fall on the shoulders of the new BBC Trust, which takes over on January 1 2007.