On Sunday, the administration was standing firm behind fair elections in the Philippines. On Monday the president suggested maybe it was enough for the two-party system to survive. On Tuesday Mr. Reagan checked himself and said he'd send out a personal envoy, Ambassador Philip Habib. Yesterday it appeared that the prior day's policy was still in effect, but it wasn't exactly sure.

What is behind this confusion of messages? President Reagan sees that the elections went wrong: they did not produce a clear winner accepted by the losers. In his view, and fairly so, this is the prescription for chaos and destabilization. What is the best way to limit the damage? A fair count is one way, but the Marcos forces resist it. Waiting for the next elections is another way but the Aquino forces reject that.

Meanwhile, gunmen -- whose can they be? -- are on the prowl: Evilio Javier, an outspoken critic of Mr. Marcos and a leading figure in the Aquino campaign, was publicly assassinated Tuesday by six thugs driving the jeep of Mr. Marcos' assembly leader. Mrs. Aquino is preparing huge street demonstrations.

Mr. Reagan's response is to dispatch yet another mission to follow that of Sen. Paul Laxalt, the warner, and that of Sen. Richard Lugar, the inspector: Ambassador Habib is to "assess the desires and needs of the Filipino people" -- as though they had not just expressed their own.

One understands why the president wishes for the convenience of having Mrs. Aquino stop complaining and rally around Ferdinand Marcos for the sake of civil peace. The bases are important; the American tie to the Philippines is important; moving on is important.

But the time for telling her to pipe down, if it ever was here, has long since passed. Mrs. Aquino has mobilized a huge portion of the Philippine electorate and brought it to the polling place. That fact cannot be ignored and the expression of those Filipinos cannot be wished away any more than they can be expected to find satisfaction in a note of congratulations from the United States calling on them to consider their vote a nice show but not binding.

The United States can live with Ferdinand Marcos -- but only if the Filipino people can live with him. Without a fair count no one can say for sure who won, but Mr. Marcos' vote-counting tactics and the gunplay bespeak a telling lack of confidence in his own popular standing. It is unthinkable that Washington should substitute its judgment favoring Mr. Marcos for what may well have been the Filipinos' judgment rejecting him.

The administration's back and forth messages have had an effect. An impression has been conveyed to the Filipinos that, cheating and thuggery notwithstanding, the Americans need Mr. Marcos for stability. This is a keen irony, since Mr. Marcos by his manner of rule is destabilizing his country; his chief leverage on President Reagan is the threat of destabilizing it further.

Mr. Reagan must move carefully, but he must move surely to undo the impression that he is choosing anyone. It is not clear that the way to do it is to make threats about aid. But it is clear that events have denied President Reagan the role he sought as the kindly impartial observer on the sidelines. He is in the thick of it.