The Premier League has to "try and make the video assistant referee better", says chief executive Richard Masters.
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."
The Premier League has previously promised to improve VAR's consistency and speed and increase communication with fans.
Six out of 10 of those fans surveyed by YouGov felt the system was working badly.
Masters said that VAR is delivering on the "principal reason" for its introduction in improving the accuracy of decision-making.
"In key match incidents we are up to 94% accuracy with officials, 97% with their assistants, so we are seeing an impact on results and a positive impact on the league table," he said.
"Obviously there are issues with consistency of decision-making and delays, which people don't like.
"But I don't think VAR is harming the product - attendances are up, TV audiences are up, the health of the Premier League is very good."
'More to be done' on racism
Statistics compiled by anti-discrimination campaigners Kick It Out suggested there had been a 43% increase in reports of racist abuse in English football in 2018-19 from the previous season.
In December, the government said it would not rule out taking "further steps" if football authorities fail to deal with racism following several high-profile cases this season.
Masters said there is "always more to be done" by the Premier League in helping to combat racism in football.
"Football has a big role to play - we are part of society and can play a role in promoting all the right messages and will continue to do that," he said.
On Monday, a fan who shouted racial abuse at players during Brighton's home Premier League game against Tottenham Hotspur in October was jailed.
"One incident of racism is unacceptable and one too many," added Masters.
"Ultimately we can't stop individuals harbouring racist or homophobic thoughts coming into our grounds or sharing them with people around them.
"It's our responsibility to make sure people who do that know there are consequences and also to put proper systems in place to deal with it when it happens.
"We need to make sure there are proper reporting mechanisms, trained stewards in place, and police if necessary, and that when perpetrators are caught they are banned from football, which we are now seeing more regularly, as well as possible criminal proceedings."
Sports minister Nigel Adams MP told BBC Sport last month that football has "far too much dependency" on sponsorship from gambling companies.
Half of Premier League clubs are sponsored by bookmakers and there are concerns about the potential impact on young fans and vulnerable people.
The Betting and Gaming Council chair, Brigid Simmonds, told a parliamentary committee on Tuesday that bookmakers are "considering" a voluntary ban on football shirt sponsorship and pitchside advertising, expanding on the whistle-to-whistle ban on television gambling adverts introduced last year.
Masters said the Premier League "welcomes" the government's upcoming review of the 2005 Gambling Act and that the league will be "willing and active participants" in it.
"Betting is a legitimate pastime - sport and betting have a long history," he added.
"The Premier League don't have any betting partnerships and ultimately it is the clubs' decision.
"I don't think if you are looking at solving the issue of vulnerable people and betting that the answer should be that the clubs can't have betting partnerships anymore - I don't think one follows the other."