An anesthesiologist convicted recently of raping a nurse while a resident at a Harvard teaching hospital pleaded innocent Friday to new charges that he raped one patient and sexually assaulted another during his residency at Waltham Hospital in 1978.

Dr. Arif Hussain, who turned himself in at Waltham District Court, two days after a warrant for his arrest was issued, was released on his own recognizance, awaiting an October 7 pre-trial conference.

He and his attorney, Kenneth R. Goldberg, could not be reached for comment yesterday.

Hussian, a former resident at Brigham and Women's Hospital, who was convicted of rape in a highly publicized trial early last June, has been working at Children's Hospital in Buffalo, N.Y., for more than a month.

Thomas Sullivan, spokesman for the New York hospital, said yesterday hospital officials were "very suprised and dismayed" to learn of the charges and Hussian's criminal record and had suspended him pending further investigation.

Hussian had been hired on the basis of three recommendations from Harvard-affilitated doctors, he added.

Dr. Benjamin Covina. head of anesthesiology at Brigham and Women's Hospital and a professor at the Medical School, and two other doctors wrote Hussian "impeccable recommendations" after the first trial ended, Sullivan said.

None of the recommendations mentioned Hussian's prior rape conviction, he added.

Covina was unavailable for comment yesterday. Sullivan did not reveal the names of the other two doctors.

The new allegations, filed by a 39-year-old Connecticut woman and a 26-year-old Boston woman, charge Hussian with rape and sexual assault on two separate occasions in 1978.

Both women said they reported the incidents to hospital authorities at the time, but neither told the police until after the earlier trial began to receive publicity.

Thomas Paxman, attorney for the Waltham Hospital, refused comment on the incident yesterday, saying, "We feel the proper forum to deal with these charges is the courtroom."