WASHINGTON (AP) _ The Transportation Department on Thursday awarded Continental Airlines the highly contested air route between Seattle and Japan, complying with a court decision directing that the route be given to the airline.

The awarding of the route, which currently is being flown by United Airlines, has been highly controversial. Continental, United and American Airlines all were seeking it on a permanent basis.

Opponents of the ruling have 10 days to petition the department to reconsider its decision, said DOT spokesman Bob Marks. He said the provision for a reconsideration request is standard in such cases.

United issued a statement saying it was encouraged that the ruling allowed for a reconsideration request, adding that the company ''strongly believes that the merits of the case clearly support United's retention of the route.''

A department administrative law judge had recommended Continental for the route originally, but a succession of senior department officials overruled the judge, chosing first United and then American.

Continental filed suit because it had not been given the route, and a federal appeals court ruled in late August that the original administrative law judge's recommendation should stand.

The department made no formal announcement on its order. But a high-ranking department official, asking not to be further identified, said Transportation Secretary Jim Burnley had wanted the Justice Department to appeal the court decision, but that Justice declined to do so.

''He believes we could have had the (court) opinion reversed on appeal,'' the official said.

The Seattle-Tokyo route previously had been flown by Pan American World Airways, but United assumed the route temporarily when it purchased Pan Am's Pacific Division in 1986.

The Transportation Department approved United's acquisition of the Pan Am routes only under the condition that the Seattle-Tokyo route be dealt with separately.

Last year a DOT administrative law judge recommended that the route be given to Continental, but that recommendation was subject to review by a senior department official designated to deal with international air routes. The official, Vance Fort, who then was deputy assistant secretary for policy and international affairs, instead recommended United keep the route.

Later, a conflict of interest problem arose because Fort at the time had been negotiating for employment at Flying Tiger Airlines, which stood to benefit depending on which airline got the Seattle-Tokyo route. No action ever was taken against Fort.

The case was returned to another administrative law judge, who also recommended that United keep the route. That decision was overruled by another senior DOT official, who recommended American.

The department was about to make a final decision when the federal court ruled on Continental's suit.