The president's office said Arundika Fernando has been "dismissed from his portfolio with immediate effect".
Fernando, a member of Sirisena's Sri Lanka Freedom Party, had claimed that seven SLFP members would leave the government soon over corruption allegations against Prime Minister Ranil Wickremesinghe's United National Party (UNP).
The SLFP runs the unity government in coalition with the UNP, though some SLFP members back a faction of the party that supports former president Mahinda Rajapaksa.
A broad working arrangement between the SLFP and the UNP to run the government is set to end in December. But Sirisena and Wickremesinghe last week announced the government's economic vision until 2020, indicating they had no intention of ending the alliance.
Sirisena fired his then justice minister Wijeyadasa Rajapakse on August 23 for criticising the government over its decision to sell a majority of shares in a sea port to China.
But after Sirisena's victory, Rajapaksa handed the party reigns to Sirisena. This caused a division within the SLFP with supporters of Rajapaksa forming a joint opposition.
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