Federal naroctics agents arrested a small-time New York drug dealer yesterday morning, shortly after he had publicly detailed his role in allegedly supplying cocaine to White House aide Hamilton Jordan.

The charges were unrelated to the Jordan case and dealt with another incident that was supposed to have taken place more than a year ago. Officials of the Drug Enforcement Administration had no comment when asked whether the arrest was made in retaliation for the accusations against Jordan.

The drug dealer, John (Johnny C) Conaghan, was picked up Friday night in Manhattan just around the corner from the Studio 54 discotheque where he allegedly administered cocaine to the White House chief of staff on a June 27, 1978, visit to the nightclub.

A DEA spokesman said Conaghan was charged with selling Quaaludes on another occasion last year. He appeared before a federal magistrate and was released on a personal bond of $10,000.

Studio 54 owner Steve Rubell, Jordan's main accuser, said he suspected the arrest was connected with "Johnny C's" appearance Thursday night on the American Broadcasting Co.'s "20/20" program.

Speaking out publicly in the Jordan controversy for the first time, Conaghan said on the broadcast that he spooned cocaine at Studio 54 last year to a man later identified to him as President Carter's top aide.

Conaghan, who frequents Studio 54, said he couldn't identify Jordan from pictures because "I've seen him only once." He said he gave the man cocaine only because Rubell asked him to. "I wasn't introduced," Conaghan said.

Rubell, who also appeared on "20/20", declared that it was Jordan. He said the White House aide "took a hit in each nostril" when Conaghan put a spoon containing the drug under his nose.

Jordan has denied ever taking cocaine. The White House has contended that his accusers in the Studio 54 case were making false charges in an effort to settle a $2.5 million federal tax evasion case against Studio 54 and its owners.

Details of the charges against Conaghan were not immediately available. Rubell said he was picked up on a warrant that was 18 months old. He said that in addition to accusing "Johnny C" of selling Quaaludes, investigators reported finding some cocaine in one of his socks when he was picked up.

DEA spokesman Robert Feldkamp said Conaghan was arrested at 2:40 a.m. yesterday, which may have been the time he was booked. Rubell said the arrest actually was made at 7:45 Friday night near Studio 54 at 8th Avenue and 53rd Street. In any case, Conaghan apparently already had been taken into custody when a Washington Post reporter arrived at Studio 54 at 1:40 a.m. yesterday to interview Conaghan. Rubell said then that "Johnny C" already had been picked up.

Justice Department sources said the arrest was not initiated by DEA, which normally does not bother with minor drug cases. They said the arrest was ordered by the office of U.S. Attorney Robert Fiske of New York's Southern District. Fiske could not be reached for comment.