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."