"The president is very fond of these birds," an official in his office told AFP, adding that he also cared for other species at the colonial-era President's House in the capital Colombo.
The macaws went missing from their aviary during the traditional New Year holidays this week. Rajapakse's office released photos of three of them on Wednesday and appealed for help to find them.
Macaws -- a species of parrot -- are not indigenous to Sri Lanka, but several pet stores import them from South America.