"I told the Prime Minister and the Cabinet last night that there should not be a political agenda in taking action against people," he said.
Addressing a gathering here, he accused the police's Financial Crime Division (FCID), Crime Investigation Department (CID) and the Commission to Investigate Allegations of Bribery and Corruption of "acting on a political agenda".
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He said he was completely angered by the recent action by the Bribery Commission to summon to court former defence secretary Gotabhaya Rajapaksa - brother of ex-president Mahinda Rajapaksa - and three former military commanders over bribery allegations.
People who led war ought not to be dragged before the court, he said.
Sirisena's comments have much resonance with the accusations by former strongman Rajapaksa and his family members of a political witch-hunt against them. The Rajapaksas have faced numerous allegations of wrong-doings and were charged in courts following which they had to spent time in police custody.
Sirisena was critical of continued police custody of some military intelligence officers charged with the abduction of a journalist.
"Human rights are applicable to everyone. They must be freed if no charges or given bail," he said.
His first public comments critical of his own administration could cause tensions in the unity government with Prime Minister Ranil Wickremesinghe's United National Party (UNP).
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