A Saudi airlines flight -- SV 788 -- carrying Rajapaksa landed at the Singapore Changi International Airport shortly after 7 pm (local time).
Approval was held up due to CBI investigation into international flying permit of Tata group-owned AirAsia India.
His whereabouts was unknown as protesters have now occupied both his office and official residence.
Sri Lanka will permit three domestic airlines to launch flights to India before they are allowed to operate on other international routes, the Civil Aviation Authority said on Tuesday.
Several countries like the United Kingdom, the United Arab Emirates, Australia and Singapore have already banned travellers from India as well as other South Asian countries.
The ex-president returned to Sri Lanka on a Singapore Airlines flight.
The President had been moved out of his residence on Friday, in anticipation of Saturday's protests.
The ATR 72-600 aircraft was accorded water salute as it landed at the Jaffna airport, about 400-km from capital Colombo.
A notification in this regard is likely to be issued by the Directorate General of Civil Aviation on Monday.
Days after its recent downgrade by the US aviation regulator, DGCA has set up two dedicated technical teams for surprise inspections on the aircraft of foreign airlines and charter firms and carry out extensive safety checks.
Forty suspects, including the driver of a van allegedly used by the suicide bombers, have been arrested in connection with the attacks which shook Sri Lanka.
Closely following Air Sahara, premier private carrier Jet Airways said on Friday that it was already "operationally equipped" to commence international operations and connect Indian metros with Sri Lanka.\n\n\n\n
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'Ex-servicemen engineers and technicians are true professionals worthy of being 'Make in India' agents. They can be trusted to bring long term dividends -- it is in their character to be long term loyalists!' says Air Marshal P V Athawale (Retd).
The man who led this journey is 50-year-old Kalanithi Maran, chairman and managing director of the Sun Group.
No one even comes close to the impact Anil Kumble has had on Indian cricket, when it comes to winning matches and series, say Aakash Chopra and Impact Index.
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