WASHINGTON (AP) _ The Navy, criticized last week for its handling of a small ship construction contract, won praise from Pentagon auditors on Monday for its handling of a larger, more important program.

The Pentagon's inspector general, in a five-page report, concluded the Navy's ''acquisition strategy and plan'' for building a new class of guided- missile destroyer ''was well conceived, properly documented and sufficiently comprehensive.''

''Our evaluation of the solicitation, evaluation and selection process (for a contractor) and contract administration showed that, as of November 1986, the contract process had been effectively managed,'' the auditors added.

The Pentagon audit was launched last summer and focused on the Navy's effort to design and build the so-called ''DDG-51 class'' of destroyers. The lead ship of that class, to be named the Arleigh Burke, is under construction at the Bath Iron Works in Bath, Maine.

The Burke-class ships are described by the Navy as destined to become the most capable destroyer ever built, fitted with the equipment and weaponry needed for anti-air, anti-ship and anti-submarine warfare. The destroyers are to include an air-defense radar system similar to that of the Navy's new Aegis cruiser.

The Navy hopes to acquire 29 of the new ships at an overall estimated cost of $26 billion.

The auditors reported the Navy's development and construction work on the new ship appeared to be on schedule, although it noted the service was experiencing some development problems with two new subsystems code-named Seafire and Racer.

The Seafire is a new ''fire-control'' system for firing laser-guided munitions, while the Racer is a supplementary power generator that relies on the exhaust heat from gas-turbine engines to drive it. The problems with those two systems have been ''clearly identified,'' the auditors wrote, and ''decision-makers were aware of these problems.''

The auditors' praise for the handling of the DDG-51 program stood in sharp contrast to a report released last week on the Navy's effort to build a new class of attack boats for its SEAL commandos.

The Navy was accused of gross mismanagement in overseeing that program, with the auditors concluding the service had paid out $10.7 million for a boat that was supposed to cost $6 million. Moreover, the first of the boats was only partially completed before the contractor went bankrupt, the auditors reported.