SLC secretary Kangadaran Mathivanan said the former skipper had told them he would not be available for the Bangladesh tournament despite being chosen for the Test matches.
"We have received an e-mail from Marvan announcing his non-availability citing personal commitments," Mathivanan told AFP.
He said the former opener, who has scored more than 5,300 runs in Tests and 8,500 runs in one dayers, had said he would, however, be available for selections in future.
Atapattu is currently in England playing for Lashings World XI.
Mathivanan said the SLC need to look at Atapattu's contract to see if the former Sri Lankan captain could be allowed to be absent from national selections.
Atapattu was overlooked by the Sri Lankan selectors throughout the World Cup in the West Indies and for the three-match series with Pakistan in Abu Dhabi.
He has not played a Test match since December 2005 and a one dayer since February this year.
The former Sri Lanka captain was drafted in the Test team last week in place of Sanath Jayasuriya who is considered only for one dayers under the new selection policy.