A recent survey from opinion polling firm YouGov showed more than two-thirds of Premier League fans questioned believe VAR has made the game less enjoyable since it was introduced into the English top-flight.
Players, managers and fans have all complained about the way the system is used, with lengthy review delays and dubious eventual decisions causing widespread frustration.
Masters, who started his permanent role with the Premier League in December, told BBC Sport that VAR would stay in the game, but he hopes it can be improved.
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"I don't think VAR has been damaging but I accept it needs improvement," Masters said.
"Scrapping it is not an option -- what we have to do is try and make VAR better."
VAR has been brought in to the Premier League to decide on goals, penalties, red cards and offside decisions.
Masters revealed to the BBC that the Premier League would discuss changes to VAR with the clubs in April.
"We are going to have a debate about what sort of VAR they would like next season and what improvements can be made to the system," he said.
"It's going to be a work in progress this season and next as we try to rebalance it so you get the positives of better decision-making and fewer of the perceived negatives about delay and sometimes confusion."
Meanwhile, in his first major media interviews, Masters said he does not believe homegrown player quotas will improve the fortunes of the England team.
The balance between homegrown and overseas players in a 25-man Premier League squad is back in the spotlight following the United Kingdom's exit from the European Union, which will affect the way clubs do their international transfer business once the transition period ends at the end of the year.
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The Football Association has previously stated in November 2018 that it favoured cutting the number of overseas players per squad from 17 to 13 with a view to boosting the chances of young English talent.
FA representatives are due to present to Premier League clubs at the league's shareholders' meeting on Thursday, and Masters says the conversation will be taken forward from there.
"We have to come up with a different system," he said.
"The FA, the EFL and the Premier League all agree that (system) shouldn't impact on the competitiveness of the Premier League, that concept of the best versus the best. Clubs should still be able to acquire the best talent and support a cohort of homegrown players coming through the system.
"We don't necessarily believe quotas are the answer."
Masters also spoke about the relationship between Premier League clubs and betting companies, following criticism of the Football Association for allowing FA Cup matches to be streamed on betting websites.
"The government deregulated gambling ... in 2005, and I think it's probably about time to have another look at it, the government are going to do that, we'll be welcome participants in that," he said.
"Our clubs have always abided by rules and regulations in relation to it, I think this area does need stronger governance, particularly to protect the vulnerable.
"I don't think the answer coming out at the end of it should be that football clubs shouldn't have shirts sponsored by gambling companies any more, but we will certainly co-operate with the review."
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