In his place, H.W. Gunadasa has been appointed as the new secretary.
De Silva, a retired administrative officer in parliament, said the letter informing him of the removal did not give a reason.
The commission was appointed on 03 March 2013 to investigate serious bribery and corruption incidents that had taken place during the previous regime.
Its tenure has been extended for one year period from 03 March this year.
The commission has completed investigations against several persons and handed over the reports to the government.
It said previously that reports into the investigations presently underway would be handed over to the president by next week.