The chairman of the Senate subcommittee that oversees the Federal Trade Commission yesterday questioned whether Michael Pertschuk, the agency's controversial chairman, can effectively run the agency any longer.

Noting that Pertschuk has been forced to withdraw from several FTC proceedings, Sen. Wendall Ford (D-Ky.), chairman of the Consumer Protection Subcommittee, said an atmosphere has been created around the agency that leaves him uncertain about Pertschuk's effictiveness.

"If anyone knew the history of FTC legislation, he should know it," Ford said in an interview, referring to Pertschuk's previous job on the Senate Commerce Committee. "But since he's been in that position, he creates an atmosphere where he has to withdraw from cases.

"That doesn't help him in his job. The decision on whether he ought to leave is up to him and the administration. Pertschuk has had a very thin line to walk.

"Whether that presents a problem only time will tell. He has the capability of running a good agency. But I'm not sure that the atmosphere he operates under will allow him to do it."

Ford's remarks come at a time when FTC is still recovering from last spring's bitter congressional fight over the commission's mandate. Congress passed authorizing legislation last spring that changes many of the agency's procedures and permits the agency to carry out most of its ongoing rule-makings and cases.

As chairman of the subcommittee with FTC oversight responsibilities, Ford played a major role in that debate and his views about the commission are particularly significant since his panel is on the verge of beginning new hearings on specific FTC matters.

For example, on Aug. 20, the subcommittee has scheduled hearings to study the commission's jurisdiction over the mobile home industry, the subject of an FTC study. Further, under the terms of the legislation passed last spring. Ford also hopes to hold hearings later this year and early in 1981 on the FTC's efforts to loosen state control over the medical and legal professions, how the commission defines "unfairness" in advertising, and the FTC's antitrust role.

But Ford also disclosed that there is one more subject the subcommittee wants to know more about. Ford is planning to ask the FTC for a full report on the circumstances surrounding the controversial FTC contract given to Harry R. Hinkes, the law judge who was given a $72,000 contract to continue hearing the FTC's landmark suit against three of the nation's largest cereal manufacturers.

Commenting on the contests of a story on the "Hinkes affair" carried three weeks ago in The Washington Post, Ford called Pertschuk's approval of the contract the kind of thing "that gives the bureaucratic process a bad name."

"We have to get a better handle on the cereals thing while its still warm," Ford said. "If they're wrong, they're going to have to start over. I'd take them to court if it were me."

Yet despite the criticism, Ford said he sees signs that the commission has listened to congressional criticism. "The attitude of the commissioners and their statements indicates they intend to narrow their rulemakings and exercise responsiblity," Ford said.

For said he has retained an "open mind" on the subjects coming before his powerful subcommittee.