The Marlins played a three-game series in Philadelphia last week but delayed their return home to Miami amid fears of a coronavirus outbreak in the team.
There have been reports of as many as 14 individuals in the Marlins camp contracting COVID-19.
MLB did not release details of the number of confirmed cases but said it was waiting on the results of "additional testing".
Manfred is confident the season can go ahead, telling the MLB Network: "I remain optimistic that the protocols are strong enough that it will allow us to continue to play – even through an outbreak like this – and complete our season."
Watch Commissioner Manfred's entire interview with Tom Verducci on MLB Tonight. pic.twitter.com/oAyJ1NoEyk— MLB Network (@MLBNetwork) July 27, 2020
However, Manfred admitted circumstances would dictate whether the season went ahead.
He said if the issue became too serious, stopping the season would be an option.
"I think that a team losing a number of players that rendered it completely non-competitive would be an issue that we would have to address and have to think about making a change," Manfred said.
"Whether that was shutting down a part of the season, the whole season, that depends on the circumstances.
"Same thing with respect to league-wide; you get to a certain point league-wide where it does become a health threat and we certainly would shut down at that point."
There have been more than 16 million confirmed cases of coronavirus worldwide, with the death toll exceeding 650,000.