The space shuttle Atlantis, scheduled for its maiden voyage Oct. 3, will carry two defense satellites in its secret military payload, the Federation of American Scientists said yesterday.

The group said the classified mission could be determined by anyone, including the Soviets, who carefully scrutinizes public documents. The group said it was revealing the payload because keeping the mission secret "inhibits public awareness and discussion of U.S. military activities in space."

The satellites, to be propelled 22,500 miles above Earth, are designed to support all three military services and carry a single channel transponder used to transmit emergency messages from the president to nuclear forces.

Although the National Aeronautics and Space Administration and Defense Department do not announce military payloads, the scientists said Atlantis' payload can be readily identified from public sources.

The group said it had determined from various military publications available to the public that Atlantis would carry two defense satellite communications system (DSCS-III) vehicles.

The most recent reference, the scientists said, was in a Dec. 28, 1984, issue of Defense Daily newsletter. It said two DCSCs would "be launched together next year on a single space shuttle mission, apparently on the Atlantis mission . . . ."

In Houston yesterday, Hughes Communications Co. announced that a primary communications circuit has failed on the Leasat 4 satellite launched from the shuttle Discovery Aug. 29.