CAPE CANAVERAL, Fla. (AP) _ The countdown began today for Thursday's launch of shuttle Atlantis, which will carry five astronauts and a secret satellite that reportedly will gather military intelligence over the Soviet Union.

The clock began ticking at 12:01 a.m. EST as NASA test director Jerry Crute issued the traditional ''call to stations'' that assembled more than 100 controllers at computer consoles in the launch control center four miles from the launch pad.

The call also was a signal for workers at the pad to begin servicing Atlantis' engines and removing work platforms from the base of the spaceship.

''We're pressing on; the countdown has started,'' said George Diller, a National Aeronautics and Space Administration spokesman.

Because the mission is classified, the Defense Department and NASA are disclosing few details of the flight, including its length and what the astronauts will be doing.

As for the launch time, sources speaking on condition of anonymity have said it should take place about 7 a.m. EST if weather and other conditions are adequate. But officials will say only that launch is scheduled for sometime between 6:32 a.m. and 9:32 a.m. Thursday. They say they will make the time public when the clock reaches the nine-minute mark.

A preliminary weather forecast for Thursday called for unfavorable conditions: overcast sky, brisk winds and possible showers.

Atlantis' crew, all military officers, planned to fly here this afternoon from their training base in Houston to make final preparations for launch. Instead of making the usual arrival comments to the news media, they have been advised to say nothing.

The crew commander is Navy Cmdr. Robert L. Gibson. The pilot is Air Force Lt. Col. Guy S. Gardner, and the mission specialists are Col. Richard M. Mullane and Lt. Col. Jerry L. Ross of the Air Force, and Navy Cmdr. William M. Shepherd.

After Atlantis reaches orbit, NASA plans only two public statements. The first, four hours after launch, will report briefly on the condition of the spaceship. The second will be a 24-hour advance notice on when the astronauts will land at Edwards Air Force Base in California.

The silence will be broken only if a serious problem develops.

Defense Department officials contend the secrecy makes it more difficult for Soviet satellites and spy ships operating off Cape Canaveral to monitor the flight and learn its purpose.

Critics argue that such secrecy is unnecessary because the Soviets, with their intelligence capabilities, already know a great deal about the mission.

In fact, the official Soviet news agency Tass said Sunday: ''The main task of the secret mission is to put into near-Earth orbit a new generation reconnaissance satellite, codenamed Lacrosse. The satellite will conduct surveillance of the territory of the Soviet Union with the help of updated radar. The Pentagon plans to deploy in the next few years four other similar spy satellites which will play the role of an 'eye' for the new strategic bomber B-2, known as stealth.''

U.S. critics also say that once Atlantis' satellite is in its own orbit, the Soviets will be able to track it precisely and know what it is doing.

Much already has been published about the satellite, based on reports from sources who say it will gather extremely sharp radar images of Soviet military targets as it follows a course that covers 80 percent of the Soviet Union.

The flight will be the 27th for a U.S. space shuttle, the third dedicated totally to the military and the second since the Challenger explosion that killed seven crew members in January 1986.

The Challenger accident kept the shuttle fleet grounded for 32 months. Discovery and a five-man crew had a successful flight that began Sept. 29.