A six-month Senate investigation of mental institutions in 12 states has found that patient abuse and neglect is widespread and that inaction by federal authorities "allows these conditions to fester."

The Labor and Human Resources subcommittee on the handicapped, opening three days of hearings on the problems of mentally retarded patients, said in a report yesterday that patients in some state institutions live in "a climate of fear and intimidation."

It said that some facilities "fail to maintain decent living conditions" and that many patients are subjected to assaults, rape and verbal abuse.

The report charged that the Justice Department had limited its enforcement efforts against patient abuse and that the Health and Human Services Department had done few audits of state facilities, although much of the care for the mentally retarded is financed through Medicare and Medicaid.

Subcommittee Chairman Lowell P. Weicker Jr. (R-Conn.), who has a son with Down's syndrome, said retarded patients "have been left in the backwaters of our conscience."

Harold Cockerham of Fort Worth told the panel how his retarded son, Chris, 13, was severely beaten last year at a Texas institution, leaving the boy with a black eye and bruises all over his body. Cockerham said he notified the Justice Department but "they refused to respond."

"I feel as though the state institutions are warehousing individuals and not caring for them," Cockerham said.

Attorney David Ferleger said the Fort Worth State School determined "no confirmed abuse" in Cockerham's case because the school could not identify who had beaten the youth. Two attendants later were indicted for the beating.

"No one knows what the rights of a parent with a child in a state institution are," Ferleger said. "States get by with violations . . . simply by making promises" to improve conditions.

Wilbur M. Savidge told the panel that weeks after his retarded son, Jonathan, 12, was placed in the Fort Worth facility, he found him on the floor "chewing on another client's urine-soaked stocking." Savidge said that his son's medical problems were neglected and that his son developed a brain infection and had to undergo surgery elsewhere that left him partially paralyzed.

Carol Sands, a deputy public advocate in New Jersey, said that her office had investigated numerous reports of patient abuse at state hospitals but prosecutors repeatedly referred these complaints to the hospitals.

The Senate report said that "states largely certify their own eligibility for federal money." It called this a potential conflict of interest, saying that states have little incentive to report violations that could lead to a cutoff of funds.

The HHS audited only 5 percent of the 2,200 homes for the retarded last year, the report said. In one case, it said, auditors found that 17 homes were substandard, but after repeated delays HHS last month approved "plans of correction" for 16 of the facilities.

The report also said the Justice Department "continues to play a limited role" in monitoring facilities for the handicapped. Although Congress in 1980 gave the department the power to file civil rights suits on behalf of patients, Justice has construed this authority very narrowly, the report said.

Many state psychiatric facilities are reviewed voluntarily by the private Joint Commission on Accreditation of Hospitals (JCAH). But the report said these surveys are announced in advance and are "largely focused on paper work requirements."

One Connecticut hospital worker told investigators that, weeks before the JCAH inspectors arrived, the patients "all of a sudden got pajamas, toothbrushes, toothpaste," and that such supplies dwindled after the inspection.

Another hospital employe was quoted as saying that, before a JCAH survey, "documentation would be added to patients' records to indicate that certain treatment procedures . . . were taking place, when in fact they were not."