Sante Alesandro Bario, a Drug Enforcement Administration agent who specialized in deep undercover operations, died today after spending four months in a coma caused by the mysterious illness that ended his controversial last case.

The events leading to his death were as bizarre as any of the criminal conspiracies he investigated in a half-dozen countries.

Bario, an Italian-born agent whose ability to infiltrate the underworld had earned a persidential achievement award, died while still under federal indictment on a charge of accepting a $9,000 bribe in an international cocaine smuggling case.

Though the much-decorated agent will not now be able to defend himself in court his attorneys are examining an appeal of his discharge by the DEA. Because of the appeal and the mystery surrounding his illness, the autopsy ot be conducted here Thursday has assumed critical importance.

Gerald Goldstein, Bario's San Antonio attorney, announced that an agreement had been reached on the autopsy between the Justice Department and Richard Ben-Veniste, a Washington attorney representing the family.

Goldstein said it was agreed that Dr. Ruben Santos, county medical examiner, will perform the autopsy with Dr.David Spain of Brookdale Hospital Medical Center, Brooklyn, N.Y., observing.

Spain is director of laboratories at Brookdale and professor of clinical pathology at New York University.

Bario was arrested Oct. 7 by fellow DEA agents who had bugged a conversation in French between Bario and a DEA informant in the Hilton Palacio del Rio hotel in San Antonio.

On Dec. 16 he choled and went into convulsions while eating a peanut butter sandwich in his cell in the Bexar County jail.

Taken to the Santa Rosa Medical Center, he never regained consciousness. A hospital lab report suggested the possibility of strychnine poisoning, but Santos ruled this out after further tests.

"We are very anxious to see the results of that autopsy," said Goldstein. But pathologists have said it is probable that trace elements of any substance which might have caused Bario's collapse would have been metabolized during his long period of unconsciousness.

The San Antonio attorney said Spain was selected because of his experience in investigating a number of unexplained deaths.

Because of the large number of narcotics offenders in Bexar County jail, Bario had first been held in the Kerr County jail in ranching country north west of San Antonio.

He was brought to the Bexar County jail in connection with a hearing and remained there in a single cell in the hospital ward.

His attorney said this made him nervous and anxious, but that he had seemed to adjust. They said he was extremely depressed in the weeks after his arrest.

His family argued for his innocence, saying he had been left out in the cold when his agency chose to believe an informer. He had told attorneys he was working on a major international investigation when he was arrested.

"Judging from the awards he received, he had a remarkable career," Golstein said.

His exploits included undercover work for the Knapp Commission which investigated official corruption in New York City and successful penetrations of the underworld leading to narcotics convictions in Mexico, Canada and several European countries.

He was acting assistant regional director of DEA's Mexico City office when he was arrested.