Chris Hughton described the actions of some Burnley supporters as "shameful" after Brighton and Hove Albion defender Gaetan Bong was booed during Saturday's Premier League goalless draw at Turf Moor.
The point edged Brighton towards Premier League safety but Hughton was unhappy with the home crowd's reaction to left-back Bong.
In January the defender made a complaint against West Brom player Jay Rodriguez - who started his career at Burnley - after a clash between the pair during a Premier League game.
Rodriguez was charged by the Football Association with using "abusive and/or insulting words which included a reference to ethnic origin and/or colour and/or race" towards Bong, but an independent regulatory commission found the accusation made could not be proven.
Bong has since stated he stands by his accusation, while the FA said it was "completely satisfied that this was a complaint made in absolute good faith".
Rodriguez, meanwhile, has continued to protest his innocence and Burnley fans sang "Jay Rodriguez, he's one of our own", leading to criticism from Hughton.
"I thought the reaction of the Burnley supporters to Gaetan every time he got the ball was shameful," Hughton told reporters. "What they should do is look at the two statements - one from the independent committee, one from the FA.
"As regards his performance, it's nothing short of what I expect from Gaetan. He is an excellent, excellent professional and a top-class individual and in a tough game like today's I thought he put in a performance as he has done for us all season, a lot of discipline and knowing he was going to have to defend very well.
"He is an incredibly disciplined and strong individual, as honest a person as you will meet. It's something that happened, it's not nice at all, but he is big and strong enough to cope with it as showed by his performance.
"I was incredibly surprised [by the boos], I certainly didn't expect it here."
Burnley are almost mathematically certain to be playing in the Europa League next season, Saturday's draw leaving the seventh-placed Clarets six points clear of nearest rivals Everton with a vastly superior goal difference.
And while Burnley boss Sean Dyche was not particularly impressed with his side's showing as their winless run stretched to three games, he is thrilled to be leading the club into Europe for the first time in over 50 years.
"I've just found that out, I hadn't looked at all the results, just a few chats along the way," Dyche told reporters.
"We've still got to make it so effectively, then it's a fantastic achievement - if we get there. You're implying strongly, and I agree, there's a massive swing involved [for Everton to catch Burnley].
"It's hard to sit here on a soft performance to question the players over the season - they've been absolutely fantastic and they've earned the right. The points we've got on the table in the Premier League, you can't cheat that."