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The world number 28 branded the ATP as a "broken system" in February after it was revealed the pandemic-hit tournament had cut prize money for singles winners from $1.35 million in 2019 to just over $300,000 this year.
The 35 year-old called for a "true audit" of the tournament to determine how much money was available and berated tennis for a "lack of transparency."
Isner revisited the issue, insisting however that the reduction in prize money was not his primary concern."I think for some of the players, it's not so much about the prize money," Isner said. "We don't really want to make it about that.
"Maybe it's about tour structure that the players would like to have better knowledge of as to why decisions are made, what went into making each decision."
Tennis finances have taken a battering since the pandemic, with the season suspended for much of 2020 and tournaments such as last year's Miami Open, and two editions of the Indian Wells Masters being scrapped altogether.
Isner acknowledged that players understood revenues had fallen because of loss of ticket sales.
"Again, it's really not about the money," he said. "Of course, we would prefer to be playing for a bigger purse.
"There's just a little bit of uncertainty about how those numbers came into play, why the prize money is what it is.
"Of course, we would like to be playing for more, but we understand with the loss of ticketing revenue, our purses are going to go down," he said.
"But there are some players that have questions about why it was down so much. The tour has implemented a strategy that is keeping the lower rounds pretty similar.
"The prize money in the quarters, semis and finals, has been chopped quite a bit. The top players in our game have taken a big hit as far as the prize money is concerned recently."
Isner, however, said the ATP Tour had been more forthright with players in recent meetings.
"Look, there’s always going to be some things that players are unhappy about," he said.
"I do think recently the players have felt like the tour has been more transparent with them. We're trying to understand the process a bit more."
Isner added that the new Professional Tennis Players Association led by world number one Novak Djokovic which he joined last year would address some of the players concerns.
"I think ultimately it could be healthy for the tour," Isner said. "Some people would definitely disagree with me."