BAA will take court action against discount airline Ryanair over £1m the airport operator says it is owed.
Ryanair will no longer receive discounts from Stansted
BAA announced it would issue a High Court writ against the company, after a 1600BST Wednesday deadline was not met.
BAA says it is owed the money for landing fees at Stansted Airport. Ryanair said it would issue its own proceedings against BAA.
Ryanair, as with other airlines, receives a discount on BAA fees during the expansion of Stansted.
A spokesman for BAA told BBC News Online the carrier will still be able to operate out of the airport, but it will no longer receive those discounts.
The Irish airline's charges stand to nearly double as a result.
Ryanair immediately hit back at BAA.
"We are issuing our own proceedings against BAA for over-charging on fuel levies at Stansted over a 12-year period," a Ryanair spokesman said.
"As BAA is already aware, our agreement on charges is very specific and expires in 2007."
The discount airline already faces a £2.74 million fine from the European Commission over the subsidies it received for using Charleroi airport in Belgium.
It is appealing against that ruling.