The scheme ( pictured), undertaken by Davis Brody Bond working with Michael Arad and Peter Walker, is facing an alleged doubling of its construction budget to $1 billion (£536 million).
This has left senior figures in the city, such as mayor Michael Bloomberg and governor George Pataki, calling for the designs to be rethought.
Davis Brody Bond was brought on to the project at the beginning of this year, just a few weeks before it agreed to join up with Aedas.
Arad won the commission for the project in 2004 following an international competition with a scheme that was budgeted at $490 million (£263 million).
The new cost, revealed in a report by the contractor Bovis Lend Lease, is blamed on the global increase in the price of steel and concrete that has affected many projects around the world.
At the time the scheme was agreed, it seemed set to be the least controversial part of the Ground Zero redevelopment.