Three American hostages alleged by their Iranian captors to be CIA agents apparently were among seven hostages not seen by American clergymen who held Christmas services at the U.S. Embassy in Tehran.

The absence of the three, according to information reaching the United States from Tehran, heightened uncertainties about why the seven were not seen by the clergymen. Iranian militants have repeatedly suggested that some hostages may be tried as spies.

The State Department has maintained that 50 hostages are being held by Iranian militants. The American clergymen, admitted to the U.S. Embassy to hold Christmas services, have said they could account for only 43 of the captives. Neither the identities nor the whereabouts of the seven remaining hostages have been officially disclosed.

Among the seven not seen, however, were the three alleged to be CIA agents, according to interviews yesterday with Americans who have spoken with the U.S. clergymen who visited Iran. The three were believed to include Thomas L. Ahern Jr., 47, who was denounced by militant Iranians three weeks ago as an alleged spy carrying a forged Belgian passport.

Two other hostages not seen apparently were William Daugherty and Malcolm Kalp, who the Iranian militants have charged were identified as CIA agents in a top-secret cable found in U.S. Embassy files.

Asked for comment yesterday on the report that the three alleged CIA agents were absent from the Christmas services, State Department spokesman Thomas Reston said, "I won't deny that story, but I won't confirm it either."

The State Department has repeatedly refused to comment on Iranian allegations that some hostages are CIA agents. American officials have also declined to confirm the identities of the 50 persons who, according to U.S. information, were seized in the embassy takeover Nov. 4.

Uncertainty about the number and whereabouts of the hostages deepened yesterday with a statement by Auxiliary Bishop Thomas J. Gumbleton, one of the clergymen who conducted the services, at a stopover at London's Heathrow Airport en route to the United States.

"As we left Tehran this morning, the students issued a statement saying there were 49 hostages inside the embassy, but six decided they did not want to attend the services," Gumbleton said.

The State Department, nevertheless, continued to insist that the correct number is 50 hostages. "We are quite positive that there are 50 American prisoners being held," spokesman Reston said at a briefing, noting that American officials have relied partly on information from 13 former hostages who were released last month. "We believe strongly that the number is 50," Reston said.

Speculation about the discrepancy between the 43 hostages reportedly seen by American churchmen and the 50 said by U.S. officials to be held captive has included the possibilities that some hostages may be ill, may have been moved away from the embassy compound or may have been singled out for harsher treatment by Iranian militants because of alleged spying activity.

The State Department on Christmas labeled Iran's refusal to make clear how many Americans are being held at the U.S. Embassy "a very cruel numbers game." Iranian Foreign Minister Sadegh Ghotbzadeh pledged Wednesday to seek an explanation for the differing counts of the number of hostages. None has been forthcoming so far.

In addition to Bishop Gumbleton of Detroit, the American clergymen who held Christmas services for the hostages in Tehran are the Rev. William Sloane Coffin of Riverside Church in New York and the Rev. William M. Howard Jr., president of the National Council of Churches.

The churchmen telephoned colleagues in the United States and provided them with lists of the hostages they had seen in Tehran. The Americans who received the calls -- including Dr. Claire Randall, general secretary of the National Council of Churches, and Bishop Thomas Kelly, general secretary of the U.S. Catholic Conference -- then sought to telephone the hostages' families. A third American who helped relay messages to the hostages' relatives asked not to be identified.

Even here, a further numerical discrepancy occurred. Although the churchmen said in Tehran that they had seen 43 hostages, the lists telephoned to their colleagues in the United States named only 42 of them. No official yesterday could explain the discrepancy.

"There's umpteen possibilities," said David Osborne, a National Council of Churches spokesman, citing various possible mix-ups.

Randall, Kelly and the third American declined, for the most part, to identify the hostages who were seen by the churchmen at the U.S. Embassy. A list of these hostages may be made public when the clergymen return, they said.

However, all three American officials confirmed that their lists failed to include Ahern, Daugherty or Kalp, the three hostages alleged by Iranian militants to be CIA agents.

Ahern's mother, Elizabeth, told The Washington Post in a telephone interview from Wisconsin that she had not been notified by church or State Department officials of her son's whereabouts during the Christmas services. Ahern, a 15-year State Department veteran, was sent to Tehran in June.

Daugherty's and Kalp's families could not be reached yesterday for comment.

One other hostage previously singled out for criticism by Iranian militants was reported yesterday to have been allowed to attend the Christmas services. Bishop Kelly confirmed that Air Force Col. Thomas E. Schaeffer, the U.S. defense attache in Iran, was present at the religious services.

Iranian students had linked Schaeffer to a purported memo offering preferential treatment for Iranian officials in exchange for intelligence information.

The most detailed U.S. listing of the hostages in Tehran was included in documents submitted by American officials to the World Court. The documents described the hostages as 28 dipolmats, 20 administrative and technical embassy staff members, and two private U.S. citizens who were visiting the embassy at the time of the takeover.

In addition to the 50 hostages, according to U.S. officials, three other American diplomats are being held at the Iranian Foreign Ministry, including Charge d'Affaires L. Bruce Laingen.