Pakistani authorities expelled the American head of a malaria research center in Lahore l ast week as a Soviet magazine said the laboratory was breeding dis ease-bearing mosquitoes for use in Afghanistan and Cuba, using unsuspected eating Pakistanis as guinea pigs.
The physician, David R. Nalin, who came here after his expulsion, said that the Soviet campaign had long roots and that pro-Soviet agents had infiltrated the laboratory and taken advantage of petty jealousies and rivalries among some of the senior Pakistani staff.
Dr. Nalin, a respected clinical epidemiologist, was also critical of what he termed the ineptitude of United States Embassy officials who were unable and in some cases even unwilling to convince Pakistani authorities that his visa should be renewed. ''It's really shocking,'' said Dr. Nalin, ''that with the $3.2 billion aid package and this wonderful new relationship we are supposed to be having with the Pakistanis, we couldn't even get a visa renewal.''
He said that as a result of his departure the center, the world's largest laboratory dealing with malaria control, would probably be closed. Target of Moscow Accusations
The 40-year-old physician said he had been aware of politically motivated opposition soon after he arrived to take charge of the project in October 1979. The laboratory and hospital had been started in 1962 as a joint project of Pakistan and the University of Maryland, where Dr. Nalin is an associate professor of international health. He said that the center's files contained reports over a period of 10 years of Moscow broadcasts alleging that the center was being used for studies in biological warfare.
Dr. Nalin reported that for the last year, as he repeatedly asked what was holding up his visa renewal, he had never been given any explanation. He said he had learned from friends in various ministries that there were objections based on reports of biological warfare research at the center.
After several delays, he said, he was officially notified at the end of January that he had to leave the country within a week or face arrest.
Since its inception the center has provided basic health care for 25,000 people and has kept detailed records on malaria. Recent studies by the center have turned up such important findings, Dr. Nalin said, as the discovery that only a tiny fraction of mosquitoes carry malaria and that they do not breed in fetid water as previously thought but prefer clean water. New Strains of Mosquitoes Sought
Another part of the center's program was the breeding of mosquitoes in attempts to develop strains of males that would mate with wild females to produce sterile larvae.
Dr. Nalin said an in-house investigation showed that two senior staff members had been spreading allegations about the center. One of these he identified as Aslam Khan, an assistant p rofessor who he said had orga nized an illegal union at the laboratory and had led strikes.
The second man who Dr. Nalin said had fomented trouble is Brig. M. A. Choudhry, deputy director, who was Pakistan's director general of health under the late Prime Minister Zulfikar Ali Bhutto and who, Dr. Nalin said, still had close ties to key officials in a number of ministries.
The situation worsened in August when Dr. Nalin tried to renew his visa. At one point he received a death threat. Questions Asked on Guest House
Some weeks later he was visited at his home by men who would not identify themselves but claimed to be Pakistani intelligence officials. He said they asked him why only Jewish scientists were being invited by the center and why the center operated a guest house in a Lahore suburb. Some left-wing magazines in Lahore reported that the center was a front for clandestine research.
Then one day last month, Dr. Nalin found a stranger rummaging through office files. He said the man identified himself as Iona Andronov and presented a card showing him to be a Moscow-based correspondent for the Soviet weekly Literaturnaya Gazeta.
He said the man told him he had come to investigate charges that the laboratory was a Central Intelligence Agency operation involved in biological warfare research. ''I told him we were such a topsecret organization that no one had stopped him from coming in and that all of our work is published in scientific journals and readily available,'' said Dr. Nalin. ''I had him escorted on a tour of our labs.'' Attack Published in Moscow
Last Wednesday, three days after Dr. Nalin left Pakistan, Literaturnaya Gazeta published an articl e say ing that a C.I.A.-backedlaboratory in Pakistan was developing virulen t strains of mosquitocarried diseases.
''Poisoners from overseas plot to infect cattle with viruses and then use the seasonal migration of herds from Pakistan to Afghanistan to start an epidemic of encephalitis in Afghanistan,'' the article said.
Dr. Nalin says that the support of the State Department has been ambiguous. He said that while John Brims, the United States Consul in Lahore, had done his utmost to press for the visa renewal, lowerechelon personnel at the embassy in Islamabad were inclined to view the issue as one of petty jealousies.
Dr. Nalin, who spent eight years working at a cholera treatment center in Bangladesh, said he had no connection with any intelligence agency. He said he thought the Soviet attack on the malaria center was intended as an answer to recent United States disclosures concerning the use of ''yellow rain'' chemical agents in Southeast Asia.
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