More than two-thirds of Premier League fans questioned believe VAR has made the game less enjoyable, a YouGov survey has found.
There have been several controversial decisions involving VAR since it was introduced to the league this season.
"I don't think VAR has been damaging but I accept it needs improvement," Masters told BBC Sport.
"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, who was appointed on a permanent basis in December after being in temporary charge for more than a year, said 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."