The U.S. Customs Service is investigating the alleged role of Panamanian strongman Manuel Noriega in the illegal shipment of American high-technology equipment through Panama to Cuba, sources familiar with the inquiry said yesterday.

The investigation, now centered in the Tampa, Fla., area, marks the third major inquiry by federal agents into alleged illegal activities by Noriega. It was disclosed earlier that the Drug Enforcement Administration in Miami and the FBI in Tampa were investigating Noriega for alleged drug-trafficking and related money-laundering.

Spokesmen for the Customs Service would not comment on the latest disclosure, but other government sources said that the high-technology items in the agency's investigation consisted primarily of computer equipment. Although the items have no intrinsic military value, sources said, they could be applied to a wide range of military and scientific uses.

"Some of it is IBM PCs," one source said, referring to International Business Machines Corp. personal computers.

Another source said that "information has been developed showing that Noriega derives personal benefit" from the shipments, through payoffs or his investment in Panamanian shipping companies. He estimated that the investigation, which involves documentary material as well as information from informants, will take four to six months.

The investigations by the FBI, Drug Enforcement Administration and Customs Service are being conducted despite a split within the Reagan administration about whether to press for the ouster of Noriega, commander of the Panama Defense Forces, the nation's sole military and police organization.

CIA and Pentagon officials reportedly have argued that Noriega's fall could endanger U.S. military bases in Panama. Even officials of the DEA have expressed reluctance about the case, noting that Noriega and his associates have supplied them with information about narcotics-trafficking.

Without the political ramifications, however, the Cuban case is a classic example of the type of high-technology flow to Soviet-bloc nations that the Reagan administration has been trying to stop. In 1982, the administration began an effort called Operation Exodus that placed new emphasis on stemming the sale of high-technology equipment and munitions to communist-bloc countries and other potentially hostile nations, including Iran and Libya.

A Senate source with knowledge of the Customs Service inquiry said that it shows greater promise of establishing criminal violations by Noriega than the drug and money-laundering cases.

Adolfo Arrocha, charge d'affaires for the Panamanian Embassy in Washington, said he had not been informed of the investigation. "I must confess that in all sincerity this is the first I have heard of this situation," he said.

The high-technology material includes recent shipments and involves the falsification of paperwork, including so-called end-user certificates, which are required documents that specify the customer to whom the equipment is being shipped, one source said.

The shipments were described as moving through the free-trade zone of Colon in Panama. "My understanding is that the stuff never leaves the airport" there and is simply transferred to Cuba-bound aircraft, a source said.

ast April, a Customs Service investigation in Miami resulted in the indictment of three men for allegedly selling more than $1 million in sophisticated computer equipment to Cuba in violation of the U.S. Trading With the Enemy Act.