Brown will still be overall director of FEMA.
Allen's appointment was announced Friday by Homeland Security Director Michael Chertoff.
The admiral had been in charge of the situation in New Orleans as an acting assistant to Brown, but now is the regional FEMA coordinator for the disaster.
Brown was sent back to Washington for what the Bush administration has called other FEMA duties. However, both Republicans and Democrats have been calling for Brown to be fired for what they call a slow and bungled response to the crisis along the Gulf coast.
Brown will still be in charge of FEMA nationally.
Earlier in the week Bush had praised Brown for the job he had done, despite Brown's admission he didn't know the extent of damage and victim displacement in New Orleans.
Brown is a lawyer by trade and a former official for the Arabian Horse Association, and critics say he had no experience in emergency management before his FEMA appointment.