The federal government filed suit yesterday against a major defense contractor and five of its former employes who took top Pentagon jobs, alleging that $485,000 in severance payments given to the men by the firm created a "conflict of interest situation" in their government service.

The civil suit, filed against Boeing Company Inc. in federal court in Alexandria, does not allege the men did anything to favor Boeing after they assumed their federal positions.

The payments were made as the men left their employment with Boeing.

Two of the defendants are still employed by the government: Melvyn R. Paisley, assistant Navy secretary for research, engineering and systems, who lives in McLean, and Lawrence H. Crandon, assigned to NATO's Air Command and Control System Team.

The three who have left government service are: Thomas K. Jones, formerly deputy under secretary of defense for strategic and theater nuclear forces; Herbert A. Reynolds, former deputy director of space and intelligence policy, and Harold Kitson Jr., former deputy assistant Navy secretary for command, control, communications and intelligence. Jones, who lives in Seattle, has been reemployed by Boeing.

A Navy spokesman, asked for comment from Paisley, said, "This is a matter between the Justice Department and Mr. Paisley, and it involves a question of law about which there is disagreement."

Crandon, who is employed overseas, and the three others could not be reached for comment.

Boeing spokesman T. Craig Martin said the Seattle-based firm would have no comment until it saw the lawsuit.

The complaint alleges that the payments, made in 1981 and 1982 and ranging from $183,000 (for Paisley) to $40,000 (for Crandon), were not paid as part of a severance policy for all Boeing employes. Rather, they were "discretionary" payments under a company policy for employes going to "certain key positions" in the federal government, the suit asserts.

The amounts paid were computed according to several factors, including the loss in pay and benefits each man would suffer by becoming a federal employe, a cost-of-living differential based on living in Washington, and in some cases, the cost of moving to the area, the lawsuit said.

The computations also included an estimate of the number of years the former Boeing official would serve in Washington, a period sometimes referred to as by Boeing as his "assignment" or "tour" with the government, according to the complaint.

The payments were "effectively supplementing the executives' pay," according to a Justice Department statement released yesterday.

Boeing "unlawfully" included these payments in administrative costs that the company said it was due under defense contracts, the suit alleges. Though the government later recouped those amounts, Boeing was "unjustly enriched" by the inflated amounts, it said.