He was taken aboard a naval vessel, SLNS Gajabahu, where he would remain until it was safe for him to return to the mainland.
The president had been using the President's House as his residence and office since protesters came to occupy the entrance to his office early April.
According to Ada Derana, the PMO said the president had informed Prime Minister Ranil Wickremesinghe of his decision, and the latter had held initial discussions with several party leaders.
Prime Minister Ranil Wickremesinghe said he would resign when all parties had agreed on a new government.
His decision coincided with the burning of his residence by angry protesters. Tens of thousands of people stormed into President Gotabaya Rajapaksa's official residence to vent their anger.
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