In a letter to Rajapaksa just days ahead of Monday's parliamentary election, Sirisena said he will not appoint Rajapaksa Premier even if the United People's Freedom Alliance (UPFA) coalition won a majority.
"There are eminently suitable seniors in the party from whom I can pick a Prime Minister," Sirisena said.
He blamed Rajapaksa for not allowing succession in the Sri Lanka Freedom Party (SLFP).
The President said he had to consent to allowing Rajapaksa to contest the August 17 election as there was a threat that the party would be split if he was not given a party ticket.
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Accusing Rajapaksa of alienating Tamil and Muslim minorities from the SLFP, Sirisena asked his predecessor not to create divisions in the party.
Sirisena was Rajapaksa's Health Minister until he came forward as the opposition unity candidate to challenge the then president last year.
Sirisena faced immediate sacking from the party only to be handed the party leadership when he defeated Rajapaksa in the January presidential election.
The SLFP is a main constituent party in the UPFA coalition.
Rajapaksa, who was the president twice since 2005 and is credited for ending country's three-decade-old civil-war with LTTE, has taken the unprecedented step of running for parliament after enjoying two terms as president.
Before Rajapaksa, none of his predecessors had stood for parliament polls after demitting the presidency.