The Tomahawk cruise missile program, which the Navy advertised as "the fastest and least expensive way to deploy additional credible deterrence against the Soviet Union," has run into trouble.

The Pentagon said yesterday the program has been restructured as a result of disappointing flight tests and production problems, delaying deployment of some versions of the missile.

Not only will there be delays, the Pentagon said, but more money than has been estimated will be needed to complete the program. There are "significant funding shortfalls in all appropriations in fiscal years 1981 through 1984," Deputy Defense Secretary Frank C. Carlucci told Congress in a letter, dated Dec. 30, that came to light yesterday, about Tomahawk problems.

Carlucci did not disclose how much more money would be needed for those years, but other sources have put the figure at $256.9 million. Carlucci said a review of the program by the chief of naval materiel "identified a number of deficiencies which require prompt resolution."

Built by General Dynamics, the Tomahawk flies to its target like a drone airplane and can be loaded with a nuclear bomb or conventional explosive. The Tomahawk is designed to fly out of submarine torpedo tubes, off surface ships or from the ground.

It has a range of about 250 miles when launched from a submarine or surface ship to hit a ship. The missile flies itself to the general area of the ship and uses onboard radar to find and guide itself to the target. The Tomahawk designed to blow up targets on land has a range of about 1,400 miles.

The Tomahawks designed to be launched from submarines or ships are the ones that have encountered the most trouble.

The version with a conventional warhead for hitting land targets was to be ready for duty, called initial operational capability, by last January, but that date has slipped to September, 1985. The duty date for anti-ship versions of the sea-launched Tomahawk has slipped from last June to March, 1984. The original target dates were stated by the Pentagon last August.

In his letter to Congress, Carlucci said the Air Force version of the Tomahawk to be launched from the ground against land targets is on schedule, as is the Navy's nuclear version of the land-attack Tomahawk. "These are the top priorities of the Tomahawk program," he wrote.

In talking about the troubled submarine and surface ship versions of the Tomahawk, Carlucci said the first would go to sea aboard the battleship New Jersey this March and in submarines this September. But this step is short of "initial operational capability," meaning fully ready for duty as opposed to being available for emergency use. Anti-ship Tomahawks on the New Jersey will not be fully ready for duty until March, 1984, according to Carlucci.

Navy Secretary John F. Lehman Jr. told Congress last year that putting Tomahawks aboard submarines and surface ships "is by far the most rapid and cost-effective way to distribute strike capability throughout our naval forces . . . .

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

Last August, Pentagon civilians fired Rear Adm. Walter Locke as head of the joint Air Force-Navy cruise missile office. Rear Adm. Stephen J. Hostettler replaced him.

Critics have said the Pentagon asked for trouble by putting cruise missiles into production before they were fully tested, something defense leaders have also done on the Pershing II battlefield missile.

The Pentagon disclosure that it has felt compelled to overhaul the cruise missile program is expected to generate sharp questioning in Congress later this year when the fiscal 1984 budget comes under review.