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.
The match referee Javagal Srinath was also seen having an animated discussion with the Sri Lankan team officials.
Sri Lanka Cricket (SLC) stoutly defended the team, saying it would defend any "unwarranted allegation" against any player.
Dinesh Chandimal of Sri Lanka hits 4 during day 4 of the 2nd Test between West Indies and Sri Lanka at Daren Sammy Cricket Ground, Gros Islet, St. Lucia, on June 17, 2018.
"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 ´under protest´ to ensure the upholding of the spirit of the game", added the statement.
Despite being at the centre of the storm, the Sri Lankan skipper put aside that enormous distraction in supporting the in-form Kusal Mendis in a fifth-wicket stand of 117 runs that lifted the visitors from the depths of 48 for four in their second innings on Sunday.
It was in March that Australia were caught tampering with the ball illegally on the third day of the third Test against South Africa in Cape Town. Pakistan eventually forfeited that game.
Steve Smith, along with David Warner, was handed a one-year ban from both domestic and worldwide cricket by Cricket Australia while batsman Bancroft was handed a nine-month suspension for their involvement in the incident.
Opening batsman Devon Smith top scored with a painstaking 61 while Shane Dowrich, fresh from a match-winning unbeaten century in the first Test in Trinidad, contributed 55.
The visiting team was charged with altering the condition of the ball by the umpires after they reviewed video of the West Indies' first innings on Friday. But fast bowler Lahiru Kumara took the most wickets, four.
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.