Khan was docked 80 percent of his match fee by International Cricket Council (ICC) referee Chris Broad on Tuesday for an outburst against outgoing batsman Matthew Hayden during the Mohali Test.
Gavaskar, who resigned as head of the ICC's cricket committee earlier this year due to media commitments, said it was strange only Asian players were being hauled up by match referees.
"If he (Khan) swore at him, if he abused him, he obviously deserves to get punished," Gavaskar told the CNN-IBN news channel.
"But let's not mince words here. Every time, it is always an Indian or a sub-continent player who gets hauled up, never the Australians."
Gavaskar said he was surprised no Australian player was summoned by the referee during the ill-tempered match which India won by 320 runs to take a 1-0 lead in the four-match series.
"There were a lot of incidents in the match," he said.
"Do you remember Virender Sehwag was given not out when everybody appealed and Ricky Ponting, the Australian captain, came from extra cover towards the umpire and kept on appealing?
"Now if that had been an Indian, the match referee would have taken him to task, fined him... This is where I think the ICC needs to actually get its act together."
This is not the first time that Gavaskar, the first batsman to score 10,000 runs in Test cricket, has accused ICC referees of being anti-Asian.
In January, he pointed the finger at South African referee Mike Procter for charging Indian spinner Harbhajan Singh with racial abuse against Australia's Andrew Symonds during the Sydney Test.
India almost abandoned the tour over Procter's ruling but agreed to continue after a separate ICC tribunal absolved Harbhajan of the charge.