"How the RAW operates and the way that the government of India operates are sometimes very different," Goonathilake told the Daily Mirror newspaper in an interview.
"This is why I said though the Indian government was for President Rajapakse, particular (RAW) officials worked against him," he added, without elaborating.
His remarks came as India's Foreign Secretary Nirupama Rao was in Colombo, the highest level visit since Rajapakse won re-election, to discuss post-war politics and reconciliation in the island.
Rao held closed-door talks with Rajapakse on Sunday and pledged more support to re-settle thousands of ethnic Tamils displaced during the final phase of fighting between troops and Tamil Tiger rebels last year.
"She expressed India’s