A New York FBI agent pleaded guilty yesterday to obstructing justice during an investigation of charges that he took a $10,000 bribe from an organized crime figure.

Joseph Stabile, 50, resigned from the bureau and turned in his badge and gun shortly before entering the guilty plea about 5 p.m. before U.S. District Court Judge Thomas Platt. He was the first active duty FBI agent ever indicted.

Stabile was first indicted in mid-September on two charges he lied about cash he allegedly took several years ago to quash gambling charges against John Caputo, a reputed member of a New York organized crime family.

That was just two days before the five-year statute of limitations for perjury ran out.

He was indicted again Monday on six counts of conspiracy and obstruction of justice growing out of the same investigation. The more recent charges described a scheme in which Stablie allegedly wrote checks to pay back a phony loan to one "Frank Roe" as a way to explain the source of the alleged bribe money. Roe then paid Stabile back in cash, the indictment charged.

Roe, a fictitious name, actually was Stabile's cousin, according to sources familiar with the case. After the first indictment, he recanted earlier false testimony and provided presecutors with documents about the phony loan transaction, the sources said.

Stabile admitted to the judge yesterday tht "Roe's" sworn statements about the transactions were true.

In return for the one-count guilty plea, the other seven felony charges against Stabile were dropped. He faces a possible five-year prison term. Sentencing was delayed for six weeks.

Thomas Puccio, head of the organized crime strike force in Brooklyn and the chief prosecutor in the case, said in a telephone interview that the Stabile case was handled like any other.

He said Stabile began plea bargaining a few days ago and "we decided because of the age of the case, and the fact that he had not other criminal (See AGENT, A12, Col. 5> record and had resigned from the bureau, to accept the plea."

The alleged bribery incident took place nearly 10 years ago, but has been widely discussed in the FBI's huge New York field office for years. For instance Anthony Villano, a now retired special agent who reportedly made allegations against Stabile, detailed the charges in a book, though he didn't name the participants.

The Stabile indictment was of particular concern to the FBI because it was the first to smear the bureau's reputation for being beyond the reach of bribes.

A spokesman for Attorney General Griffin Bell emphasized yesterday that the FBI had operated fully with Justice Department investigators since the investigation was reopened last fall because of new testimony.