Liverpool's Italian forward Mario Balotelli was the most abused player with some 8,000 posts, of which more than half were racist in nature.
His team mate Daniel Sturridge and Arsenal's Danny Welbeck were also regular victims.
"I was shocked when I saw that," Liverpool manager Brendan Rodgers told reporters on Friday.
"One message is one too many. We support all organisations trying to stamp this out."
More than 95,000 other messages were directed at clubs, with Chelsea and Liverpool featuring most frequently.
"Kick It Out" director Roisin Wood told the BBC the level of abuse was "truly staggering".
"We must do all we can as a collective to protect those who are on the receiving end of discriminatory abuse," she said.
The organisation wants to form a group with representatives from football, social media and the police to tackle racist, sexist and homophobic abuse on platforms like Twitter.
(Reporting by Steve Tongue, editing by Ed Osmond)
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