Raytheon will also continue technology refresh work.
The systems are designed to defend ships against cruise missiles and integrate with programmed anti-air warfare stand-alone defensive systems.
Raytheon will perform 90 percent of the work in San Diego and the remainder in Tewksbury, Mass. and Portsmouth, R.I.
The Navy expects work to be complete by September 2012.
The Naval Sea Systems Command in Washington is the contracting activity.