The same charge was levelled against Australia batsman Cameron Bancroft who was caught on camera rubbing a piece of sandpaper on the ball against South Africa in March.
Sri Lanka captain Dinesh Chandimal has been charged with altering the condition of the ball in the second Test against West Indies, the International Cricket Council (ICC) said on Sunday.
Angry Sri Lankan players refused to take the field on the third day of the match in St Lucia on Saturday, delaying the resumption of play for almost two hours, after the ICC said umpires Aleem Dar and Ian Gould had changed the ball and awarded West Indies five penalty runs.
"Sri Lanka captain Dinesh Chandimal has been charged for breaching Level 2.2.9 of the ICC Code of Conduct," the ICC tweeted.
The breach relates to changing the condition of the ball. The same charge was levelled against Australia batsman Cameron Bancroft who was caught on camera rubbing a piece of sandpaper on the ball against South Africa in March.
Sri Lanka Cricket (SLC) said the team had denied any wrongdoing.
"SLC advised the team to take the field to ensure the continuity of the match and wish to commend the decision taken by the team to continue with the game 'under protest' to ensure the upholding of the spirit of the game," the cricket board said in a statement.
"The team management has informed us that Sri Lankan players have not engaged in any wrongdoing.
"SLC shall take all necessary steps to defend any player, in the event any unwarranted allegation is brought against a member of the team."
Sri Lanka were 34 for one in their second innings at the end of the third day, trailing West Indies by 13 runs after the hosts were dismissed for 300.
West Indies won the first Test of the three-match series by 226 runs.