Speaking in parliament for the first time since being elected as an MP in August, Rajapaksa saw the danger of senior commanders being hauled before a war crimes probe.
"It is my view that these officers should be granted service extensions by the government until the danger abates," he said.
Rajapaksa said when they retire they lose the institutional backing and protection provided by the military.
He was critical of the decision by his successor Maithripala Sirisena to release some of the LTTE suspects and delisting of some of the Tamil diaspora organisations listed by him as terrorist groups.
In response, Sirisena told the House that the release of LTTE suspects and de-proscription of organisations were based on state intelligence reports that they no longer posed threats to national security.
Sri Lanka has come under pressure to conduct a probe into alleged human rights violations and war crimes committed during the final phase of the conflict by both government troops and the LTTE.
The over three-decade Sri Lankan civil war killed about 100,000 people.
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