An independent counsel agreed yesterday to dismiss criminal charges against two former aides to Henry G. Cisneros. As a result, the onetime housing and urban development secretary will stand trial alone in September on allegations that he lied to FBI background investigators about his relationship with an ex-mistress.

John D. Rosales and Sylvia Arce-Garcia, who worked for Cisneros at HUD, were indicted along with him in December 1997 on charges they conspired to conceal details about "hush money" allegedly paid to Cisneros's former mistress, Linda Jones. They were to go on trial with him Sept. 7 in U.S. District Court.

During a brief court hearing yesterday, prosecutors announced they will dismiss charges against Rosales and Arce-Garcia within six months after the case against Cisneros is concluded, provided neither commits any crimes during that period. Under the arrangement, the former aides admitted no wrongdoing and made no agreement to cooperate with independent counsel David M. Barrett.

Rosales, now an assistant to housing secretary Andrew M. Cuomo, said after the hearing that he was "pleased with the outcome." Arce-Garcia remains a top aide to Cisneros, who is now president of Univision Communications Inc. in Los Angeles. She did not attend the proceedings but released a statement afterward in which she declared: "I can't explain how relieved and happy I am that this two-year nightmare is over."

Lawyers with Barrett's office declined comment. The move enables prosecutors to focus solely on Cisneros and allegations that he made false statements about the extent of his payments to Jones before his confirmation as HUD secretary in 1993. Cisneros has pleaded not guilty to 18 felony charges.

Cisneros and Jones began their affair in 1987, while he was mayor of San Antonio. He made the relationship public the following year. By 1991, they had broken up and Cisneros reconciled with his wife.

During the background check that preceded his confirmation as housing secretary, Cisneros told the FBI that he had never paid Jones more than $10,000 a year and that the payments had stopped. In fact, prosecutors said, Cisneros paid Jones more than $250,000, including $73,000 after he took control at HUD.

The prosecution's star witness against Cisneros is Jones, who secretly recorded numerous telephone conversations in which they discussed the financial arrangements. But Jones, who formerly went by the name of Medlar, admitted in a recent pretrial hearing that she edited some tapes and then passed them off as originals. Defense lawyers are trying to keep the tapes out of the trial, but Judge Stanley Sporkin has yet to make a final decision on that issue.

According to prosecutors, Cisneros directed Rosales and Arce-Garcia to conceal information about his relationship with Jones when they were questioned by the FBI during his background check. Both had worked for a communications company owned and run by Cisneros before joining him at HUD.

Rosales and Arce-Garcia were charged with one count each of conspiracy. Rosales also had faced two counts of making false statements. Sources familiar with the investigation said Barrett's office had hoped that they would become government witnesses.

CAPTION: Former HUD chief Henry G. Cisneros faces trial Sept. 7 on charges he lied about payments to an ex-mistress.