A top FBI executive is moving over to run the Drug Enforcement Administration on an interim basis, in a move some disappointed DEA officials say foreshadows an FBI takeover of the agency.

Francis M. (Bud) Mullen, the chief criminal investigator in the FBI, is to take on the new assignment next week, while remaining as one of three executive assistant directors of the bureau, officials said yesterday. He is to explore how the two agencies can cooperate on the drug problem, one said, emphasizing that no final determination on reorganization has been made.

DEA administrator Peter B. Bensinger announced Tuesday that he is resigning July 10 at the request of the Reagan administration. Reagan Justice Department officials have been critical of the federal drug enforcement policy of the Carter administration, and Attorney General William French Smith has announced that he wants the FBI to take more responsibility in the drug area.

Despite disclaimers that no decision has been made on merging the DEA into the FBI, some DEA officials said Mullen's appointment even if only on an interim basis, will be demoralizing to drug agents because it will be viewed as subordinating the DEA to the bureau, which has always looked down on the drug agency. "There are a lot of long faces over here," on DEA headquarters official said yesterday.

Attorney General Griffin B. Bell studied the merger issue early in the Carter administration, but decided against it, aides recall, because neither agency was enthusiastic. Instead, he set up DEA-FBI task forces in New York, Los Angeles and Chicago. Only the Los Angeles taks force is still operating.

Rudolph W. Giulianai, associate attorney general who has been studying the DEA reorganization, said in a recent interview that he recognizes that there would be difficulties merging the DEA into the FBI. "The two biggest obstacles realistically are the effect on morale and the personnel problems. Would the down time be worth it?"

The FBI has had a historical aversion to narcotics work. The late J. Edgar Hoover feared his agents might be corrupted by the enormous amounts of cash handled by narcotics traffickers, and shunned a role for his agency. The bureau always has prided itself on being an "excepted" service, with higher standards for its 8,000 special agents than those of the regular civil service. The DEA's 2,000 agents, on the other hand, work under civil service regulations.

When mentioning the need to involve the FBI in the drug traffic, Justice officials like Giuliani cite the bureau's financial expertise. DEA officials counter that they have led the way in winning forfeiture of assets seized from drug criminals. Bensinger said in an interview the day he announced his resignation that he felt such forefeitures eventually could finance the federal drug enforcement effort.

Any merger of the DEA into the FBI probably would require legislative action, because the DEA has authority to operate internationally, while the FBI is a domestic law enforcement agency. Some DEA officials reportedly have questioned whether the FBI could work effectively overseas because of past reports of abuses by the FBI and CIA.