Deputy Minister of Higher Education and Research Sudarshani Fernandopulle, Deputy Minister of Rural Economic Affairs Lasantha Alagiyawanna and Deputy Minister of Ports and Shipping Eric Prasanna Weerawardena decided to resign from their respective portfolios.
"We were much hurt by President's comments both as the leader of our party and the leader of the UPFA," Fernandopulle told reporters.
Alagiyawanna said they had accepted ministerial position following a party decision to be part of the minority prime minister Ranil Wickremesinghe's government.
Sirisena's decision angered all his backers who had accused Rajapaksa's government of nepotism, corruption and curbing civil freedoms.
On Tuesday, Sirisena in a televised address had said he was helpless as a majority in the party wanted him back.
Sirisena had said he was coming under increasing pressure from his Sri Lanka Freedom Party (SLFP) and its broader United People's Freedom Alliance (UPFA) coalition to allow Rajapaksa to contest election.
"Mahinda Rajapaksa who lost on January 8, will be defeated again. I will not make him the Prime Minister even if my party wins the election," Sirisena had said.
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