An American and a West German were arrested yesterday by the FBI in Fort Lauderdale, Fla., and accused of conspiring to smuggle nuclear materials and components of the top-secret U.S. cruise missile to the Soviet Union.

The suspects, labeled by an FBI official as "enemy agents," were identified as Carl John Heiser III, 32, of Highland Beach, Fla., and Carl Lutz Weischenberg, 33, a West German who lives in Freeport, Bahamas.

After what the FBI called a "lengthy" investigation, the two men were arrested without incident at the Fort Lauderdale airport as they arrived in Heiser's Cadillac to drop off Weischenberg for a flight to Freeport.

They were formally charged as acting as unregistered foreign agents and were held without bond pending a hearing on Friday.

FBI sources said the investigation is continuing and other charges may be made.

In a statement from Washington, FBI Director Clarence M. Kelley, quoting from a bureau affidavit filed in connection with the case, said Weischenberg "reportedly offered Heiser $250,000 to take components of the Cuba." In addition, Kelley said, Weischenberg tried to purchase uranium oxide, thorium and other weapons-grade nuclear materials for the Soviet Union.

The 14-page affidavit, file in Florida by FBI special agent Bill J. Windland, said Heiser told an informant as recently as June 30 that he was "involved in international espionage with the East Germans and the Russians."

The informant said Heiser had bought a 1969 Chris Craft Commander boat and docked it behind his residence to use in transporting cruise missile components to Cuba. He quoted Heiser as saying he had "something real big going down" shortly.

Coincidentally, June 30 was the day that President Carter announced he was halting production of the B-1 bomber in favor of deploying the pilotless, 21-foot-long nuclear-tipped cruise missile, which is being tested and is expected to be combat-ready by 1980. The main components are being built in California, the state of Washington and Michigan. It is being tested in California.

It was not clear from the affidavit where or from whom Heiser planned to get the missile components or what the components would be. An FBI spokesman said. "We don't know the answer yet."

There is a "suspicion" that one or more other persons may be involved, the spokesman said, emphasizing that the probe is continuing.

The spokesman said it was also not known whether any of the components had been obtained by Heiser or other persons acting on his behalf. The FBI affidavit quoted Heiser as saying on March 28 that the operation would take place in "about four months," meaning late July. Heiser reportedly identified the contact in Cuba as a "very important person" who "controls intelligence operations."

The Associated Press reported that Heiser's mother, Dorothy Heiser, in a telephone interview from her Florida home, said her son had been to Germany during the past year.

Asked where in Germany, she said, "East Germany, the one that's on our side, isn't it?" She said she knew nothing about the charges except that "the FBI came out this morning an informed us, "adding that the situation seemed "crazy."

THe FBI affidavit quoted a reliable foreign informant as saying Weischenberg is one of 12 defendants awaiting trial in West Germany on charges of high treason involving transmission of West German data processing materials to Soviet bloc countries.

It said Weischenberg and Heiser had obtained secret U.S. military information over the past two years and passed it on to Soviet and East Germany agents, with Heiser working on "shopping lists" provided by Weischenberg. The affidavit said the material included IBM cards manuals and tapes, Memorex computer programs, Bendix computer drive shafts and nuclear fuels.

The affidavit also quoted Weischenberg last August as saying the Soviets wanted to purchase uranium, thorium and other nuclear materials "in any quantity available," for cash on delivery.

The affidavit said Heiser had voluminous records of purchase orders in his residence, and the FBI said yesterday it obtained documents from the residence under a court order.

The FBI said Heiser is unemployed, although his mother was quoted as saying he runs a collection agency in oca Ration, Fla.