A confidential Pentagon study warned the Navy almost two years ago that it would run into trouble on its attack submarine program if the service did not change course.

The study, obtained in an unclassified form by The Washington Post under a Freedom of Information Act request, said, in effect, that the Navy seemed determined to go to the poor-house in a Cadillac.

Today, this is indeed the case, with the added problem that the Navy and its submarine builder, Electric Boat, Co., are at an impasse over who should pay for this "Cadillac" of attack submarines, the 688 class.

General Dynamics on Monday said its Electric Boat division would halt work on the subs on April 12 because it could not afford to keep spending its own money on the program when the Navy had not paid $544 million in disputed back bills.

The company said in a letter to the Navy obtained yesterday that "the Navy's material breaches of the 688 contracts" not only have made the construction program untenable but also "have materially increased the cost" and "seriously delayed" the Trident nuclear missile submarine, a linkage that had not been made previously.

Long before the Navy's relations with its submarine builder deteriorated to their present low point, a Pentagon submarine warfare specialist looked at the trend lines and sounded an alarm.

Instead of building a variety of relatively inexpensive submarines for specialized jobs, wrote Robert M. Chapman on July 26, 1976, while serving as an undersea warfare specialist in the Pentagon's research office, the Navy has opted for a do-everything attack submarine in ordering the 688 class built.

"The emerging Los Angeles [688] class has become all three options rolled into one: the anti-submarine-warfare killer submarine; the independent forward area submarine, and the defender of the surface fleet," wrote Chapman, who has since left the Pentagon.

He said "this country does not appear to have the resources, either in terms of dollars or skilled manpower," to execute the Navy plan to build 90 copies of a submarine as fancy as the 688 class attack boat.

Although the federal government has tried to overcome the shortage of skilled shipbuilders by setting up training programs, the results "have been very disappointing," he wrote. Thus, the 688 submarine program looked overambitious to Chapman from both money and manpower standpoints.

The submarine force building program has reached a critical point." Chapman warned, because "the resources available in the future are inconsistent with stated" goals of building a fleet of 90 attack submarines as sophiscated as the 688 class on order.

The Navy, he said, must find a way to get more "bang for the buck" by improving on the 688 design, with a better nuclear power plant the most promising place to start. "The current philosophy that all attack submarines must do all things well" may have to be abandoned, he wrote.

He recommended that the Pentagon explore new avenues to reduce the weight and size of submarines like the 688 to give th nation "a more effective, more affordable submarine force."

The Navy leaders, despite such warnings, are sticking to their present course of building giant submarines like the 688 class attack beat and Trident missile submarine, both of which are encountering delays and cost problems at Electric Boat.

Gordon W. Rule, who formerly was the Navy's overseer for shipbuilding contracts, said last night that the problems encountered on the 688 and Trident subs stem from the Navy's refusal to follow the "fly before you buy" principle.

The Navy, he continued, should have finished one sub of each class to learn the problems before writing the contracts for the following snubs. The shipbuilders should be paid their actual costs on each lead ship instead of being forced to work within a fixed estimate, he added.

President Carter said on Jan. 27 that "part of the problem" at Electric Boat and other defense contractors stems from tinkering with the design after construction has started. Defense Secretary Harold Brown said much the same thing last week, declaring the government must take some of the blame for the shipbuilding problems because "we have not written the contracts carefully enough" nor "disciplined ourselves to minimize changes" once construction is under way.

Electric Beat has complained that the Navy drove up its costs on the 688 class subs by making 35,000 changes, one reason the yard has threatened to call it quits.