European airline pilots began a two-month boycott of flights to the Soviet Union today as other aviation personnel announced separate curbs in protest of the downing by Soviet jet fighters of a South Korean jumbo jet in which 269 persons were killed.

In action paralleling that of the pilots, West Germany and Spain today formally suspended civilian air traffic to and from the Soviet Union for two weeks beginning Thursday. The move, implementing a decision reached by most of the NATO allies last week, drew a protest from the Soviet ambassador in Bonn. Japan also joined the two-week ban.

Today's announcements followed more than a week of harsh rhetorical attacks on Moscow as western governments grappled with the nature of their response and intense pressure from among commercial pilots helped rapidly produce the ban on flights to Moscow. Thirteen of the 16 NATO members are expected to join the two-week, two-way boycott recommended by the United States when it takes effect. Greece, France and Turkey have refused to join the action.

Greek opposition, meanwhile, prevented the issuance by the 10-nation European Community of a strong condemnation of the Soviet destruction of the plane. After a stormy foreign ministers' meeting in Athens, the community expressed its "deep emotion" at the fate of the airliner without mentioning the Soviets.

The statement urged the International Civil Aviation Organization, which meets in Montreal in emergency session Thursday, to investigate further the circumstances of the downing of the Korean plane, special correspondent Andriana Ierodiaconou reported. It also supported proposals outlined by French Foreign Minister Claude Cheysson for steps to ensure greater security for international civilian flights.

Here in Bonn, government spokesman Peter Boenisch announced today that West Germany would suspend Aeroflot landing rights in this country and cancel all Lufthansa flights to Moscow for two weeks.

Foreign Minister Hans-Dietrich Genscher said in a radio interview that the 14-day interruption of air traffic should not be construed as a sanction but rather "a political signal" urging the Soviet Union to make amends and ensure that such a tragedy never occurs again.

Soviet Ambassador Vladimir Semjonov protested the planned boycott by NATO nations in a meeting at the Foreign Ministry in Bonn today, a ministry spokesman said. The Soviet envoy reportedly said his country reserved the right to take measures in response, the spokesman said.

In Tokyo, the Japanese government toughened its sanctions to bring them more in line with those of the NATO countries, Washington Post correspondent William Chapman reported.

The Cabinet approved Prime Minister Yasuhiro Nakasone's recommendation to ban all civil aviation flights between Japan and the Soviet Union for two weeks beginning Thursday. Modest sanctions imposed last week had banned Soviet charter flights to Japan and had appealed for a public boycott of Aeroflot flights to Japan.

In Dublin, the Irish Cabinet planned to consider at its regular Tuesday meeting what government sources said was an almost certain 14-day suspension of Aeroflot stopovers on its long-haul flights to Cuba and other destinations. The British ban itself is expected to severely curb Aeroflot refueling at Shannon Airport, one of the Soviet carrier's largest installations outside Eastern Europe, because of the bar on traversing British airspace.

Commercial pilots in Italy, the Netherlands, Norway, Denmark, Finland, Sweden and Spain joined the two-month ban recommended last week by the governing body of the International Federation of Airline Pilots Associations. Danish pilots, however, recommended reducing the ban to two weeks because the move "primarily will hurt western airlines." Britain took the lead within the federation, announcing its 60-day ban immediately, effective last Friday.

Pilots of Air France, the French national carrier, said today they would boycott the airline's flights to Moscow beginnng Tuesday, although other reports quoted Air France spokesmen as saying flights to Moscow would be maintained with crews drawn from nonmembers of the pilots' federation.

Norwegian air traffic controllers announced a boycott of all Aeroflot flights to Norway effective tonight, a spokesman announced in Oslo, and Swedish air controllers fixed a week's boycott beginning Monday.

Genscher stressed today that the plane incident must not be allowed to hinder long-term relations between the Soviet Union and western countries in cultural, economic and political areas.

The West German government, while prepared to take tangible steps to express outrage toward the Soviet action, is acutely concerned about shielding the Geneva negotiations on medium-range nuclear missiles in Europe from the harsh tensions ignited by the airliner incident.

Chancellor Helmut Kohl received a personal letter from President Reagan Thursday explaining that the United States would seek to ensure that disarmament talks would not be affected by western measures protesting Soviet behavior.

West Germany was also eager to develop an allied consensus in any punitive action to be taken against Moscow so that it would not be isolated and compelled to bear the burden of possible Soviet retaliation.

Following the Soviet invasion of Afghanistan, the Bonn government of then-chancellor Helmut Schmidt felt deceived and embarrassed when it ended up as the only European ally to abide by the Olympic Games boycott instigated by the Carter administration.

In addition, West Germany feels more vulnerable than other European allies because it depends to a large extent on Soviet cooperation to maintain a smooth flow of air and ground traffic to Berlin.

West German officials say they are confident that Moscow will not pull out of the Geneva negotiations because the additional stigma of aborting arms control talks would inflict even greater damage to the Soviet image abroad.

Kohl government officials said they were highly pleased by the close consultations with Washington during the current crisis. They said they believed that European concerns were taken into account by Reagan's refusal to adopt more extreme measures such as an economic boycott that the allies would have rejected.

At the same time, they said U.S. pleas for concrete action were answered by the allies with the two-week ban endorsed by most NATO members.