Chandimal is accused of breaching Level 2.2.9 of the ICC Code of Conduct for "changing the condition of the ball".
Going into Sunday's (NZ time) third day, the tourists were instructed to play with a different ball and the hosts were awarded a five-run penalty, as umpires Aleem Dar and Ian Gould ruled Sri Lanka had altered the condition of the ball during the West Indies' first innings.
Sri Lanka refused to take to the field after umpires instructed that the ball be changed - with a new one to be selected by the Windies - before the start of play.
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There were animated discussions involving match referee Javagal Srinath and the Sri Lankan pair of coach Chandika Hathurusingha and team manager Asanka Gurusinha.
Officials penalised the Sri Lankans five extra runs for the holdout, but the Sri Lankan camp maintained that despite eventually taking the field, the team was still playing under protest.
"The team management has informed us that Sri Lankan players have not engaged in any wrongdoing".
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As the West Indies players were waiting on the ground, the Sri Lankan team didn't turn up even as both umpires were waiting.
The umpires suspected that the visitors' skipper Dinesh Chandimal changed the condition of the ball and made a decision to change it which didn't go down well with the team.
"If there are any, Code of Conduct charges will follow as per usual at close of play", tweeted the ICC. Pakistan eventually forfeited that game.
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This was the second such instance within three months, after the Australians were found guilty of ball-tampering in South Africa in March during the third Test between the two nations.
Steve Smith and David Warner were stripped of the captaincy and vice-captaincy respectively and banned from playing global cricket for 12 months.
Sri Lanka on Saturday night said that it will defend the National cricket team over ball tampering allegations which surfaced in the West Indies.
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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.