Article 2.2.9 of the ICC's code of conduct relates to changing the condition of the ball in breach of clause 41.3 of the ICC Standard Test Match, ODI and T20I playing conditions.
Sri Lanka Cricket released a statement saying its players "have not engaged in any wrongdoing" and that the team had taken to the field "under protest".
The tourists eventually chose to play following lengthy discussions between match referee Javagal Srinath and Sri Lanka's coaching staff.
Sri Lanka captain Dinesh Chandimal will face charges of changing the condition of the ball at the end of the ongoing Test against West Indies but plans to contest the allegations after pleading not guilty.
The umpires had also levelled a penalty of five runs against Sri Lanka 10 minutes before the start of the play on Day 3, and made a decision to change the ball.
Minister of Sports Faiszer Musthapa, and the Competent Authority of Sri Lanka Cricket (SLC), Kamal Pathmasiri in collaboration with the SLC CEO Ashley De Silva and Chandima Mapatuna, Head of International Cricket of SLC conveyed to the team management that SLC will take all necessary steps to defend any player, in the event any unwarranted allegation is brought against a member of the team.
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The Sri Lankan board sent out a statement defending its players.
"They say something, maybe, that meant the ball needed to be changed; maybe it was the shape".
Second time around the tourists lost Kusal Perera for 20 en route to 34 for one - a deficit of 13.
That match was the only Test in the game's history to be forfeited after Pakistan refused to return to the field.
Lahiru Kumara was again their most outstanding bowler, constantly threatening with his pace and aggression to finish with figures of four for 86 and lift his wicket tally to 11 halfway through the series.
On the field, Sri Lanka clawed their way back into the match to restrict West Indies' lead to 47 after the hosts resumed on 123 for two replying to 253.
Mendis touched a leg-side delivery from Jason Holder through to wicketkeeper Shane Dowrich when on 14 but was reprieved as the West Indies captain had overstepped the front crease.