President Maithripala Sirisena met with top bureaucrats on Tuesday and told them to "fulfill their respective duties and responsibilities" without disruption while the prime minister and cabinet were prevented by the court from carrying out their work.
On Monday the Court of Appeal denied Rajapakse the authority to act as prime minister and stripped his cabinet of their powers, giving Rajapakse until 12 December to prove his legitimacy and that of his government.
The country has been in a crisis since Sirisena replaced Prime Minister Ranil Wickremesinghe with Mahinda Rajapaksa last month, and then issued an order dissolving parliament and called for a general election.
Speaking during the Special Sri Lanka Freedom Party convention held in Colombo on Tuesday, President Sirisena said he will abide by court rulings and urged all political party leaders to support him to end the on-going political impasse.
Sri Lanka's toppled premier likened the president to Hitler on Tuesday as he demanded to be reinstated, nearly six weeks into a paralysing political crisis in the Indian Ocean nation.
The Supreme Court this week is also expected to rule on whether Sirisena's decision to dissolve parliament in November was constitutional.
The Sirisena-Rajapaksa combine has boycotted six motions in the legislature since the unrest began.
Sirisena came to power in 2015 on a pledge to uphold democracy and stamp out corruption, but his popularity has been hit by a crisis many say he triggered because of personal differences with former Prime Minister Wickremesinghe.
"The president has to appoint me prime minister as I command a majority in Parliament", he said.
The Tamil MPs last week pledged support to sacked premier Wickremesinghe, further weakening the position of the Sirisena-Rajapakse coalition.
The decision by the Court of Appeal on Monday is the latest setback to Sirisena and Rajapakse, whose attempt to take power almost two years ahead of the next elections plunged Sri Lanka into crisis.
He said Wickremesinghe destroyed him too to a certain extent. "I still hold the majority of the house".
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