The Navy's newly renovated battleship New Jersey is steaming around the Far East armed with two types of Tomahawk cruise missles that may not work and a computerized guidance system for them that has been "decertified" because it is unreliable.

Continuing problems in the Tomahawk system were disclosed last week, when the Navy asked Congress to reprogram $39.5 million in fiscal 1983 funds, taking money that was to purchase operational missiles, similar to those aboard the battleship, and transferring it to pay for more research and development on the missiles and their guidance system.

"They tried to go to production too soon," was the way one Capitol Hill source described the Navy's situation.

Nonetheless, according to a Navy spokesman, the New Jersey is carrying with it a classified number of conventionally armed, Tomahawk antiship missiles (TASM) and Tomahawk land attack missiles (TLAM-C).

Both those missiles, Rear Adm. Daniel L. Cooper told the House Armed Services Committee Tuesday were deficient.

The "seeker and missile software" for the TASM requires modification and the TLAM-C needs such "significantly improved capabilities," according to Cooper, that its initial operating capability has been put off two years to 1985.

The TLAM-C, in particular, needs "additional development and testing of the guidance system, and incorporation of a new warhead," according to documents supplied Congress.

The TLAM-C and TASM cruise missiles aboard the New Jersey, a Navy spokesman said Friday, represented weapons the service describes as having "initial fleet capability." Last January, when problems with the cruise missiles first surfaced publicly, then-Deputy Defense Secretary Frank C. Carlucci said the New Jersey's missiles would not be fully tested but would be available for emergency use.

The Navy Tomahawk has had a long history of problems.

In his presentation to the House committee, Cooper ticked them off saying "subsequent to approval of the fiscal 1983 budget, Tomahawk test flight failures, manufacturing deficiencies, delays in flight tests and decertification of the theater mission planning system (TMPS) caused the secretary of the Navy to direct an independent review of the complete program."

The findings, Cooper said, "require prompt resolution," beginning with the TMPS computer software, which serves not only to plan the flight of each missile but also directs the command, control and communication of the missile.

The Tomahawk can be launched from a ship or a sub and is designed to hit other ships or land targets, with either a conventional or nuclear warhead. It flies at subsonic speeds, controlled by a computerized radar system which guides it to its target.

In another reprogramming presented to the House on Tuesday, Cooper asked for an additional $11.7 million to increase special testing associated with the vertical launch system needed to place the Tomahawk aboard submarines.

"Without these additional funds," Cooper said, "new construction submarines will be delivered with a partial or untested cruise missile launch system."

The Navy said it would pay for the additional research on the cruise missile development program by canceling production of 69 missiles which had been planned for fiscal 1983. Another 16 TLAM-C missiles that were to be put into operational use are now to be used for testing, according to the Navy.

Navy Secretary John F. Lehman Jr. has been a big booster of the system, telling Congress in 1982 the Tomahawk system aboard submarines and ships "is by far the most rapid and cost effective way to distribute strike capability throughout our naval forces . . . .

"The current five-year plan," Lehman said, "includes measures to deploy more than 100 ships with Tomahawk capability."

That year, however, difficulties with the contractor, General Dynamics Convair Division, forced a delay in that schedule and required the Navy to ask for more money.