He accused former defence secretary Gotabhaya Rajapaksa and head of the state intelligence Kapila Hendawitharana of being responsible for those incidents.
Fonseka was speaking to the media after giving a statement to the CID yesterday (25) with regard to the abduction and torture of journalist Keith Noyarh 10 years ago.
However, the ex-defence secretary has pointed his finger at Fonseka over the incident.
The minister also said the military officers loyal to him too, had been tortured while under arrest.
Everything happened because of the then government, and it was the government and Gotabhaya Rajapaksa who became concerned, and the Army did not become troubled, he said.
He added that he would not go after the media despite the mud being thrown at him even now.