"Sri Lanka captain Dinesh Chandimal has been charged for breaching Level 2.2.9 of the ICC Code of Conduct", the ICC tweeted.
Umpire Aleem Dar inspecting the ball Sri Lanka were deemed to have tampered.
Players finally took the field at 10:50 a.m., but the Sri Lanka fielders subsequently left the field in protest, remaining just beyond the boundary in discussions with team management, while match officials also huddled in conference.
After initially appearing to be prepared to resume the match, the Sri Lankan cricketers then hesitated even as they were making their way out to the middle.
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The International Cricket Council announced on Twitter that Chandimal had been charged for "breaching Level 2.2.9 of the ICC Code of Conduct".
The Sri Lankan Biard ensured that they "will take all necessary steps to defend any player, in the event any unwarranted allegation is brought against any members of the team".
The video evidence will be used in the hearing which will also be attended by the match officials as well as the Sri Lankan team management.
They penalised Sri Lanka before play on Saturday with a change of ball and the award of five runs to the West Indies.
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"I think that everyone is a bit jumpy and walking on eggshells, especially after what happened in South Africa".
But an hour has gone and we are still no closer to the start of the third day's play as West Indies trail Sri Lanka by 135 runs with eight wickets in hand. By not pleading guilty to the charge laid by the ICC for "changing the condition of the ball", Chandimal will attend a hearing by match referee Javagal Srinath after the conclusion of the Test.
Following the Bancroft incident, which resulted in three Australian players being handed lengthy bans by their own board, the ICC made a decision to consider severe sanctions against ball tampering.
The latest incident was akin to the 2006 one where Pakistan chose not to return after tea on day four against England at The Oval, after umpire Darrell Hair changed the ball and awarded five penalty runs.
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Opener Devon Smith fell for 61, having added only eight to his overnight half-century, while wicketkeeper/batsman Shane Dowrich followed up his century in the first Test with 55.