Alfred F. Dougherty Jr., a top-ranking official of the Federal Trade Commission, has resigned charging that the agency has begun to give in to its political opponents.

Dougherty, director of the FTC's Bureau of Competition, protested in his letter of resignation that "an air of calculating caution has spread within the commission" in response to the congressional campaign to limit the FTC's power.

His resignation, effective June 30, became known yesterday when the FTC released copies of his May 20 letter of resignation to FTC Chairman Michael Pertschuk, and Pertschuk's reply.

Pertschuk denied yesterday that any differences between the commissioners and the FTC staff were due to a loss of nerve in the face of the long Congressional assault on the agency.

"That's his characterization," said Pertschuk. He said that he and other commissioners have become more demanding, challenging the staff for more evidence and stronger analysis before taking action.

"If he means that we're ducking cases, the answer is no," said Pertschuk.

Pertschuk met yesterday, afternoon with Dougherty; Perry Johnson, the bureau's deputy director; and members of the bureau's staff to reassure them that the commission isn't backing away from the monopoly and merger issues that concern the bureau.

Johnson, a member of the commission staff since 1974, will replace Dougherty as acting director of the competition bureau.

While challenging Dougherty's characterization of the commission's current attitude, Pertschuk praised him in a memo to the FTC staff, saying that Dougherty had molded the bureau of competition "into a well-managed, well-focused and dynamic force" to protect consumers and businesses.

Dougherty praised Pertschuck even more fully in his letter of resignation, but said he has become "increasingly doubtful" that the commission can achieve "the goals to which you and I committed ourselves."

Some of Dougherty's associates say his letter was meant in part as a public message to the commission to check what he fears is a drift to the right.

Pertschuck and other commissioners have acknowledged that the commission has become more careful in bringing actions. This has been more evident in the past year as the congressional debate over the agency's role intensified.

Congressional negotiators finally agreed a month ago to authorize FTC operations for another three years, but only after imposing restrictions on several current FTC inquiries and trimming the agency's authority generally.

In his letter, Pertschuk agreed that the FTC had encountered a more hostile reception from Congress, the courts and the public than he or Dougherty had expected three yeaers ago when Pertschuk became chairman. ". . . from time to time we have been forced to reef our sails to avoid foundering in the storm," Pertschuk said.

But he insisted in an interview that the coming months will show that Dougherty's fears are unfounded.

Recently the commission turned down recommendations from the Bureau of Competition to block two mergers, one involving wine companies in California, the other between Pillsbury and Fox Pizza. The commission concluded that the economic issues in these mergers weren't large enough to justify action.

On several other instances recently, the FTC commissioners have pushed the staff hard to justify actions such as the proposed requirement that used-car dealers tag vehicles as "OK," "Not OK" or "We Don't Know." But, Pertschuk said, the bottom line is that the used-car regulation was approved -- not shelved.