Lokuge said he would invite Sri Lanka Cricket (SLC) officials and the national selection panel to discuss the matter.
"Chandana had told the press that he was treated unfairly. So we have a duty to look into his grievances.
If corrective action is needed, we will take them," Lokuge said.
He said it was most likely the president himself would take part in the meeting which is expected before Monday.
Chandana, 35, on Wednesday said he was quitting international cricket in disgust and accused national selectors of treating him shabbily.
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The leg-spinner said his omission from the World Cup and the World Twenty-20 Championships had forced him to take the decision.
Rajapakse had previously intervened when veteran Sanath Jayasuriya announced his retirement in 2005.
Chandana scored 1,627 runs and took 151 wickets in 147 one day internationals between