A source at Defence Estates, the MoD's property arm, said the architect, Taunton firm Pick Everard, would not lose the commission but a second practice would probably be hired to "beef up" the designs. The building is intended to accommodate staff after the fleet headquarters is moved from London.
David Phipps, senior estates adviser at Defence Estates, sent a fax to Portsmouth council's planning department last week about the decision. The fax said: "This action is felt appropriate in order to take on board the comments received in connection with elements of design. Following consideration of these comments it is anticipated that a revised scheme will be submitted shortly."
As the proposed five-storey headquarters is a government building, Defence Estates does not need planning permission but must consult the council.
Several local bodies have made it clear that they are unhappy with the scheme. Criticism has focused on the building's corridors and atrium.
John Pike, head of conservation and design at Portsmouth council, said: "There was concern about the design from local organisations and this is the result. It is all about getting the right design of building for such a prominent site."
The withdrawal of the designs means that the scheme is unlikely to be completed by its deadline of the end of 2003. Defence Estates now expects the completion date to be in 2004.
Architectural watchdog CABE said the decision to rethink the design showed that architectural issues were moving up the MoD's agenda. A spokesperson said: "This shows that the MoD is taking the Better Public Buildings campaign seriously."
Pick Everard was unavailable for comment.