In February it was reported that Hamilton, 33, had a reported substance abuse relapse and had met with MLB officials in New York to discuss "a disciplinary issue."
An arbitrator ruled last week that Hamilton had not violated his drug-treatment program and could not be disciplined by Major League Baseball.
That prompted Angels general manager Jerry Dipoto to say he had serious concerns about Hamilton’s “conduct, health and behavior," with Angels president John Carpino saying it "defies logic" that Hamilton's behavior did not violate the drug program.
MLBPA condemned anonymous leaks of Hamilton’s relapse, saying they were "cowardly" and undermined the "integrity of our collectively bargained agreements and in some instances have been wholly inaccurate."
"I have no reason to believe the Angels did anything inappropriate. Confidentiality is an important component of the drug program," Manfred said to the Los Angeles Times. "Unfortunately, the more people that know about something, the less likely it is that it's going to stay confidential.
Manfred confirmed that Hamilton is still in baseball’s drug-treatment program, but declined to say if he has entered a rehab clinic.
"Issues like the Hamilton situation are difficult for everyone involved," Manfred said. "I'm sure the club and the player will find a way to work together moving forward. I don't think it's as serious a problem as it might appear."
Hamilton has two seasons left of a five-year $125 million contract and is set to make $25 million this season.
He is expected to be out until May after having surgery to repair the AC joint in his right shoulder.
- Scooby Axson