"I have no reason to believe the Angels did anything inappropriate," Manfred said during a visit to Safeco Field for Wednesday night's game between the Angels and Seattle Mariners.
An arbitrator ruled last Friday that Hamilton, who had reported a relapse in his battle with substance abuse, had not violated his drug-treatment program and could not be disciplined by Manfred.
Under baseball's drug program, investigations into whether a player has violated policy are supposed to remain confidential unless and until a player is suspended.
Hamilton's situation became public knowledge after The Times reported on Feb. 25 that he had met with MLB officials in New York regarding "a disciplinary issue," citing "a person with direct knowledge of the situation."
Angels General Manager Jerry Dipoto confirmed that Hamilton had gone to New York. CBS Sportsline and the New York Daily News — also citing unidentified sources — said the issue involved a cocaine and alcohol relapse.
National pundits blamed the Angels for leaking information, with some citing as their incentive the money they would save if Hamilton was suspended and had to forfeit a portion of his $25-million salary for 2015. But Manfred said he did not feel any pressure to investigate the club.
"Confidentiality is an important component of the drug program," Manfred said. "Unfortunately, the more people that know about something, the less likely it is that it's going to stay confidential.
"I think we will work hard going forward to make sure we do everything we possibly can to retain the type of confidentiality that has generally been a hallmark of our program."
Manfred also expressed confidence that the Angels and Hamilton, who is rehabilitating from right-shoulder surgery in Houston and has not been with the club, can mend a relationship that was strained by the relapse.
In the wake of the arbitrator's ruling, Dipoto issued a statement saying the Angels "have serious concerns about Josh's conduct, health and behavior," and team President John Carpino said it "defies logic" that Hamilton's behavior did not violate the drug program.
The comments came off as insensitive to many who believe that Hamilton, who overcame a harrowing addiction to cocaine and alcohol to become a five-time All-Star with the Texas Rangers but has struggled in two seasons with the Angels, should be treated with more compassion.
"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."
Manfred would not say if Hamilton had entered a substance-abuse rehabilitation clinic, but he did say Hamilton is "in the program," and added, "we have the very best doctors involved, and I hope it turns out to be a positive result."
The Angels have a six-game trip to Texas and Houston next week with an off day Thursday before the Houston series, giving them ample time to meet with Hamilton to discuss his injury rehab and how he might be integrated back into the lineup.
Manager Mike Scioscia said that, as of Wednesday, there was no plan to meet with Hamilton or for Hamilton to visit the clubhouse at Minute Maid Park. But he did not rule out the possibility.
"He's in Houston, we're going to be there, so we'll see if we can connect and see exactly where he is," Scioscia said. "Right now the most important thing for Josh is to make sure he's getting the help he needs, getting the support. That's where our concerns are. We'll touch base with him."