BATH – Bath Iron Works is not affected by a stop-work order on the Navy’s program to build a new generation of speedy and maneuverable warships.

The Navy ordered defense contractor Lockheed Martin to stop work for three months on its second ship in the Littoral Combat Ship program because it’s running over budget. The Navy cited “significant cost increases” in a statement on Friday.

Lockheed Martin’s first ship, which is 70 percent complete, is being built at Wisconsin’s Marinette Marine Corp. The stop-work order applies to Lockeed Martin’s second ship, which is under construction at Louisiana’s Bollinger Shipyards Inc.

General Dynamics is building its own Littoral Combat Ship that reflects an entirely different design at Alabama’s Austal USA shipyard. Bath Iron Works, a General Dynamics subsidiary, is lead contractor on that project.

The Littoral Combat Ship has been fast-tracked because the Navy wants a smaller ship that can operate in coastal waters.

The ships are designed to hunt submarines, locate underwater mines and chase small boats in shallow waters close to the shore.

The first ship that’s being built at Marinette in Wisconsin is now projected to cost as much as $410 million, compared with initial projections of $234 million, said Howard A. Rubel, an analyst at Jefferies & Co.

The Navy took action, Rubel said, to “signify its displeasure with the substantial cost overrun on the program.”

The ship that’s being built at the Austal shipyard in Mobile, Ala., is about 50 percent complete, said Bath Iron Works spokesman Jim DeMartini. He said it is too early in the process to tell how much the Austal ship, which is due to be launched later this year, will cost when done.

The Navy could choose the Lockheed Martin or the General Dynamics design, or it could choose to build both designs. The Navy wants to build 55 of the ships, which are a big part of the Navy’s overall goal of a 313-ship fleet.