The comedian died on 4 September, aged 81, a week after she stopped breathing at the Yorkville Endoscopy centre.
A report released by the Department of Health cited multiple errors, including failing to detect Rivers' deteriorating vital signs during the procedure.
Negligence has not been alleged.
The New York medical examiner's office ruled Rivers died of brain damage due to lack of oxygen during the procedure examining the back of her throat and vocal cords
The death was classified as a "therapeutic complication", meaning it was a known risk.
The comic had been sedated with the anaesthetic propofol, however the report said there there were inconsistencies recorded in its dosage.
It added there was no record staff at the clinic weighed Rivers before administering the drug.
'Misconduct and mismanagement'
Hypoxia - brain damage caused by lack of oxygen - and cardiac arrest are extremely rare, but potential side effects associated with high doses of propofol.
Patients usually sign a waiver before surgery to confirm they understand the risks, but the report said there were no records of medical consent for all the procedures performed.
Investigators said the clinic "failed to identify deteriorating vital signs and provide timely intervention" in Rivers' case.
They also noted a staff member took pictures of the comic without her consent while she was under anaesthesia, in violation of the clinic's mobile phone policy.
Rivers daughter Melissa said she was "outraged by the misconduct and mismanagement" that occurred and wanted to ensure it does not happen again with any other patient.
Her lawyers are investigating the circumstances surrounding her mother's death.
As a result of the state investigation, the Department of Health and Human Services has given Yorkville Endoscopy until 7 January to correct deficiencies to avoid losing accreditation to the government's Medicare programme covering the elderly.
The clinic told NBC it had submitted a plan to officials addressing all the issues raised. It added the physicians referenced in the report no longer provided services there.
The New York clinic where Joan Rivers suffered a cardiac arrest during a medical procedure failed to follow standard protocols while treating her, state health investigators have said.