The chief accountant of the General Accounting Office has told Congress that vital components of the District of Columbia's new but faltering $38 million computerized accounting system are so "woefully inadequate" that the city probably cannot operate it.

This conclusion by D.L. Scantlebury, the chief accountant, supports the contention of beleaguered city officials that they are not primarily at fault for the operational shortcomings of the system, as claimed two months ago by American Management Systems Inc. of Arlington, which designed the system.

On one level, Scantlebury's assessment is the latest move in a long-running and bitter intramural dispute among the agencies involved in ordering, designing and operating the system, which was mandated by Congress to bring order to the city's chaotic financial records.

But at a higher level, it could delay implementation of the most important element in the city's long range financial program -- entry into the private money markets where loans are cheaper than they are at the U.S. Treasury, from which the city has borrowed since before home rule.

The assessment could prolong the debate about whether the city's books are ready to face the scrutiny of the agencies that give credit ratings to municipalities. It gave city officials a Pyrrhic victory in the war of words with AMS.

At the center of the controversy is the Financial Management System, known as FMS, a comprehensive, computerized program for recording, controlling and cross-checking all city revenues and expenditures.

It issues checks, keeps track of purchase orders and shows how much money the city is authorized to spend at any given time -- all operations that were previously erratic or inaccurate under the city's old mostly manual system.

FMS has been in place for 14 months; its screens and terminals are fixtures in offices throughout the city government. But city officials have said that it takes constant care and adjustment, is beyond the capabilities of the District's own personnel and does not produce bookkeeping data in the formats the city needs to manage its money.

A vital part of the system is the 5,000-page "system documentation" library, which in effect explains what the system does and how it does it.

"The provision of adequate, usable documentation for the FMS system will require substantial time and effort, and it is important to understand that the FMS system is incomplete and unacceptable without such documentation," he wrote in a letter to Ira S. Shapiro, staff director of the U.S. Senate subcommittee responsible for District affairs.

American Management Systems designed the system at a cost of $38 million, paid jointly by Congress and the city. By Oct. 1 of 1979, the system was supposed to be in place and fully operable by the District. At that point, the city's independent auditors would be able to audit the District's books. Soon thereafter, the city could enter the private bond market.

But the system has not functioned adequately and in September, American Management Systgems announced that the FMS could never function properly in the "operating environment" of the District government.

They declined to bid on a new contract to help operate it, leaving the District government unable to run a system on which it is now totally dependent without expensive assistance from private computer consultants.

Scantlebury's letter said that no contractor other than AMS could do that work, because of the gaps in the documentation. But last week, the city let a $1 million contract to Computer Sciences Corp. of California to provide the assistance that AMS said would be futile.

Jan M. Lodal, executive vice president of AMS, who has made no secret of his exasperation with both the city and the GAO accountants monitoring the development of FMS, said yesterday that he had not seen the letter and could not comment on its substance.

David Splitt, director of the District's Office of Documents, who is one of the city's key figures in grappling with the problems of FMS, said that "adequate software documentation is the single most important factor in the District's being able to use and maintain FMS. It's the key to FMS being able to work, and we have been saying for months that the documentation was inadequate."