In Meteorology Department director-general S.H. Kariyawasam's apology, after an outcry from nationalists, he said he was sorry "if any insult was caused to King Mahasen or the country's proud history."
Cyclone Mahasen killed 18 people earlier this month in Sri Lanka, Bangladesh and Burma, the BBC said.
The apology was sent in a letter to the National Council for Local Irrigation Culture, who noted King Mahasen's contributions to the irrigation culture of the island, the online newspaper Colombo Page said.
Nationalist monks, and Sri Lankan President Mahinda Rajapaska were critical of the decision to name the cyclone after the Sinhalese king, saying he brought prosperity to the island nation, the BBC reported.