Dr Mark Chavez, of California, entered the plea during an appearance in US District Court in Los Angeles on Wednesday. At sentencing, he could face up to 10 years in prison.
Another Californian physician charged, Dr Salvador Plasencia, has pleaded not guilty, as has co-defendant Jasveen Sangha, who authorities said was an illicit supplier of the drug and was known as the "ketamine queen."
The pair are scheduled to go on trial in March next year.
Perry's live-in personal assistant, Kenneth Iwamasa, who admitted to injecting Perry, and the alleged middleman who said he obtained ketamine from Sangha, have already pleaded guilty to charges they faced.
In court on Wednesday, Chavez, 54, stood at a podium and answered "yes, your honour" to a series of questions.
The defendant admitted to obtaining ketamine with a fraudulent prescription written for another patient and that he knew the drug was intended for Perry.
He also acknowledged providing ketamine, a short-acting anaesthetic, to Plasencia, and that he understood it should only be administered under medical supervision with proper safety equipment nearby.
According to court documents, Plasencia administered ketamine to Perry at the actor's home and supplied vials that were injected by the assistant. Plasencia's lawyer has said his client properly prescribed and administered ketamine to Perry.
Perry died in October 2023 from "acute effects" of ketamine and other factors that caused him to lose consciousness and drown in his hot tub, according to a December 2023 autopsy report. He was 54.
The actor had publicly acknowledged decades of substance abuse, including during the years he starred as Chandler Bing on the hit 1990s television sitcom Friends.
Chavez pleaded guilty under an agreement with prosecutors, who offered him lesser charges for his assistance in their case against Plasencia and Sangha.
"He has accepted responsibility. He is cooperating," Matt Binninger, Chavez's attorney, said in court.
Chavez has relinquished his medical licence and remains free on bond until sentencing.