The administration warned Congress yesterday that recent votes rejecting a proposed arms sale to Saudi Arabia may have encouraged Iran to intensify attacks on neutral ships, including two Saudi vessels "operating peacefully" in the Persian Gulf.

In a statement that White House officials said was intended to be part of a renewed campaign for the arms sale, spokesman Larry Speakes said:

"We are concerned that the recent action of Congress in rejecting an arms sale may have created the misperception that the U.S. commitment to freedom of navigation in the Gulf and Saudi self-defense has diminished.

"Any such view would be gravely mistaken. We strongly support Saudi Arabian self-defense."

The House and Senate voted overwhelmingly last week against the sale, valued at $354 million, of Stinger antiaircraft, Harpoon antiship and Sidewinder air-to-air missiles to Saudi Arabia. Early next week, Reagan is expected to veto the congressional resolutions of disapproval.

Although the president did little lobbying on the issue, the White House is gearing up to block a veto override. In each chamber vote against the sale, opponents of the measure mustered more than the two-thirds majority that would be required to overturn a veto.

At least five oil tankers have been hit by Iran and Iraq this month in renewed attacks, according to Reuter news service, which reported that more than 200 merchant ships have been attacked or damaged since the Iran-Iraq conflict began in September 1980.

Speakes said that, within the last eight days, two Saudi tankers have been struck by Iranian aircraft "in what appears to be an intensification of strikes on neutral ships operating peacefully in the Gulf."

"To avoid miscalculation, we reemphasize the importance we attach to the principle of freedom of navigation and the free flow of oil, as well as our determination to maintain open access through the Strait of Hormuz," Speakes said.

He added that "the U.S. continues to seek the earliest possible end to the Iran-Iraq war. At the same time, we will support the individual and collective self-defense efforts of our friends in the region and will continue to consider an expansion of the Iran-Iraq war to the Arab Gulf states to be a major threat to our interests."

The Saudis already have shoulder-fired Stinger missiles, and the new ones would not be delivered until 1989. But Speakes said the congressional vote would have an immediate impact on the war because "its a question of perceptions . . . of U.S. resolve to support its friends in the region."

Failure to send the weapons, he said, "would send the wrong signal at a critical time." A White House official said the statement was also intended to reassure the Saudis of administration support.