The purge affected by Sirisena claimed the posts of nine frontline backers of Rajapaksa as SLFP organisers.
He appointed new electoral and district organisers during a meeting held at the President's official residence, party officials said.
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Sirisena succeeded Rajapaksa as leader of SLFP after he unexpectedly beat the latter in the January 2015 election.
Before the election, Sirisena was Rajapaksa's health minister. He challenged Rajapaksa in the snap election called by the former strongman with support from then opposition United National Party (UNP).
Since winning the presidency, Sirisena and the UNP of the current Prime Minister Ranil Wickremesinghe banded together to form the unity government.
However, Rajapaksa loyalists were believed to have formed opposition to the government with support from a section of SLFP members.
The Rajapaksa faction have carried out several campaigns against the Sirisena government including last month's five-day protest march.
Sirisena has accused the Rajapaksa clan of trying to divide and weaken SLFP.
The action to remove Rajapaksa backers is being seen as a move by Sirisena to consolidate his position as the party leader ahead of next months 65th anniversary convention of the party.
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