Rajapaksa, his wife and two bodyguards departed aboard a Sri Lankan Air Force plane, an immigration official told Reuters.
A government source and a person close to Rajapaksa said he was in Male, the capital of the Maldives. The president would most likely go to another Asian country from there, the government source said.
The immigration officer said the law does not allow authorities to prevent a sitting president from leaving the country.
Rajapaksa was set to step down as president on Wednesday to make way for a unity government after thousands of protesters stormed his official residence and that of the prime minister on Saturday, demanding their removal.
The president has not been seen in public since Friday.
Sources close to Mahinda Yapa Abeywardena, the Speaker of the Parliament of Sri Lanka, said he had not yet received any message from Rajapaksa. The source close to Rajapaksa said he would send a letter of resignation later on Wednesday.
Prime Minister Ranil Wickremesinghe has also offered to resign. If he does, that would make the president acting president until a new president is elected, according to the constitution.
Parliament will meet again on Friday and will vote five days later to elect a new president, Abeywardena has previously said.
The Rajapaksa family, including former Prime Minister Mahinda Rajapaksa, has dominated the politics of the country of 22 million for years and many Sri Lankans blame them for the current problems.
The tourism-dependent economy was hit hard by the Covid-19 pandemic and a decline in remittances from overseas Sri Lankans, while a ban on chemical fertilizers hurt agricultural production. The ban was later overturned.
The Rajapaksas introduced populist tax cuts in 2019 that impacted public finances, while shrinking foreign reserves curtailed imports of fuel, food and medicine.
Gasoline is strictly rationed and there are long lines at stores that sell cooking gas. Headline inflation reached 54.6% last month and the central bank has warned it could rise to 70% in the coming months.
HIDDEN
Mahinda Rajapaksa, the president’s brother, resigned as prime minister in May after protests against the family turned violent. He went into hiding at a military base in the east of the country for several days before returning to Colombo.
In May, the Rajapaksa government appointed Mohammed Nasheed, the Speaker of the Parliament of the Maldives and former president, to help coordinate foreign aid to crisis-stricken Sri Lanka.
That same month, Nasheed publicly denied allegations that he helped Mahinda Rajapaksa secure a safe haven in the Maldives.
Protests against the Sri Lankan government have simmered since May, but broke out again last Saturday as hundreds of thousands of people poured into Colombo, occupying key government buildings and residences.
On Tuesday, immigration officials prevented another brother of the president, former finance minister Basil Rajapaksa, from flying out of the country.
It was not clear where Basil Rajapaksa, who also holds United States citizenship, wanted to go. He resigned as finance minister in early April amid violent street protests against fuel and food shortages, and resigned his seat in parliament in June.