But, Muhundan will continue to be its CEO.
A closest associate of prime minister Ranil Wickremesinghe, he was in charge of the UNP communication unit during the past elections.
Rajapakse, the new appointee, is a coordinating officer to the president.
Telecommunications ministry secretary Wasantha Deshapriya has sent a letter to ICTA, informing it of the decision.
ICTA has been asked to explain Muhundan’s appointment to the institution.
Two other directors, lawyer Upul Kumarapperuma and lawyer Chanuka Wattegama too, have been removed from their positions.
However, minister Harin Fernando has told them not to resign, promising that he would discuss with the prime minister and arrange for their continuation at ICTA.