Clubs returned to socially distanced training in small groups this week and the league hope to begin playing the remaining 92 matches on June 12 or 19.
Premier League players and staff have been checked for the coronavirus, with six people testing positive including Watford defender Adrian Mariappa.
“We’ve taken the first step. It’s great for everybody, including the fans, to see our players back on the training ground,” Masters told BBC Sport on Friday.
Masters said he was “as confident as we can be” that teams would be able to start in June.
Asked if the Premier League had an exact date for a return, Masters said the organisation had to be “flexible”.
While the top tier is taking baby steps towards emulating the Bundesliga’s return to action, leagues in France, Scotland and the Netherlands have been abandoned because of the pandemic.
Masters said he recognised the need for “contingency plans” and admitted “curtailment is still a possibility”.
Watford captain Troy Deeney and Chelsea midfielder N’Golo Kante have both opted against returning to training over health fears.
Culture Secretary Oliver Dowden said phase two, the return of contact training in elite sports, could get government approval “later this week”.
But Masters admitted the Premier League will not approve that step until it is safe.
“We wouldn’t have taken the first step to get back to training if we weren’t convinced we had created a very safe environment for our players,” he said.
“It is the first step and we have to be sure when we go to contact training we have completed those processes.
“We have done everything we possibly can to make return to training as safe as possible.
“We think it is safe to return. We have to respect players’ decisions not to return to training. I would be comfortable to return to training.”
Matches will be played behind closed doors due to the virus, but Masters said the Premier League want games to be staged at clubs’ normal stadiums rather than neutral venues, which was the original suggestion.
“We’re talking to the authorities about that,” he said.
“I do believe we can appeal to fans not to congregate outside football grounds or go to other people’s houses to watch football matches in contravention of government guidelines.”