It was initially expected that Sri Lanka Cricket (SLC) would ask the 37-year-old right-hander to show cause for his decision to stay out of the team despite being included in the 15-man squad.
"We will speak to him on his contractual obligations (with Sri Lanka Cricket), but stop short of taking disciplinary action," a senior SLC official told AFP.
Jayantha Dharmadasa, the SLC chief, said they would go easy on Atapattu.
"We will have to consider Marvan's services to the country as a player and captain," he said suggesting that the national governing body would not pursue any drastic action.
Atapattu is one of SLC's 18 contracted players.
The last of his 88 Tests was in December 2005 and he was overlooked for the entirety of the World Cup and the subsequent series with Pakistan in Abu Dhabi.
He was recalled to the side for the Bangladesh series before announcing his surprising pullout last week, citing personal commitments .