He was referring to the Supreme Court's summoning of the 11-member select committee to appear before it with regard to the motion of impeachment against the island's first ever woman chief justice Shirani Bandaranayake.
"No outside entity has any authority over the Speaker, parliament or any committee appointed by the Speaker", Rajapaksa who is the elder brother of the Sri Lankan president said.
Rajapaksa's ruling came as the Leader of the House and senior minister Nimal Siripala de Silva raised a privilege matter in the House.
De Silva said that petitions filed in the Supreme Court against the select committee were a violation of privileges.
The 11-member select committee is probing 14 charges against Bandaranayake, 54, who also became the island's first ever woman Supreme Court judge in 1996 before being appointed chief justice in 2011.
The next hearing is scheduled for December 4.
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The motion seeks removal of the chief justice in the culmination of a month long clash between the judicial and executive wings of the government.
The judiciary cited political interference violating its independence as the reason for friction.
The opposition dubs the government move as a political witch hunt in order to undermine the independence of the judiciary.
The government's move was criticised by the US, Commonwealth and international rights watch groups as an action undermining the independence of judiciary.