A New York drug dealer who allegedly administered cocaine to White House aide Hamilton Jordan was indicted yesterday on conspiracy charges for other transactions involving narcotics.

A federal grand jury in Manhattan accused John (Johnny C) Conaghan, 27, of Oceanside, N.Y., of conspiring to distribute both cocaine and Quaaludes on repeated occasions over the past 2 1/2 years.

Government prosecutors insisted that the case has no connection with the Justice Department's investigation of Jordan, President Carter's chief of staff. Attorney General Benjamin R. Civiletti is considering whether to name a special prosecutor to pursue that inquiry.

Conaghan has been free on personal bond since he was arrested Oct. 6, shortly after he publicly alleged that he supplied Jordan with cocaine at Studio 54, a trendy New York discotheque.

U.S. Attorney Robert B. Fiske Jr. of New York said yesterday's indictment stemmed from an investigation that began 4 1/2 months ago, well before the government was appraised of any allegations involving Jordan.

The grand jury accused Conaghan of conspiring with other individuals, both known and unknown to distribute narcotics from Jan. 1, 1977, until the moment he was arrested. He was picked up by federal narcotics agents just around the corner from Studio 54 and initially was charged with selling Quaaludes to an undercover agent in April 1978.

The indictment did not name any of Conaghan's supposed confederates nor did it state where he allegedly sold the drugs. One Justice Department official, however, told a reporter recently that Studio 54 was Conaghan's "principal base of operations."

In addition to the conspiracy charge, Conaghan was accused in eight other counts of distributing narcotics. The grand jury said he sold quantities of cocaine in May and June 1977, June 1978, June 1979 and on Oct. 3, 1979. He was charged with selling Quaaludes in April 1978 and June and July 1979.

Assistant U.S. Attorney Dominic Amorosa said a 10th count in the indictment accused Conaghan of possessing cocaine last Oct. 6 with intent to distribute it. At the time of his arrest, investigators said they found four or five packets of cocaine in one of Conaghan's socks. They told a federal magistrate that he had been planning to sell it at Studio 54.

Speaking out publicly in the Jordan controvery for the first time earlier this month, Conaghan said he spooned cocaine to a man later identified to him as Jordan at Studio 54 on June 27, 1978. Conaghan said he did so at the behest of Studio 54 owner Steve Rubell.

Justice Department sources said the June 1978 sale of cocaine alleged in the indictment dealt with another transaction not involving Jordan.

The Justice Department also has been investigating allegations that Jordan sniffed cocaine on a visit ot Los Angeles in October 1977. He has denied ever using the drug. 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 tax evasion case against the discotheque and its owners.

The conspiracy and cocaine charges against Conaghan carry maximum penalties of 15 years in prison and a $25,000 fine. Maximum penalty for selling Quaaludes is five years in prison and a $15,000 fine.

According to Amorosa, the investigation that led to Conaghan's arrest and indictment also prompted the arrest Oct. 3 of Mitchell Yuspeh, 35, of New York City, on charges of conspiring to distribute Quaaludes. Federal narcotics agents said they seized approximately 60,000 Quaaludes and $15,000 in cash from Yuspeh's apartment when he was taken into custody Yuspeh is free on bail.