Zoo keepers and residents helped capture Rajapaksa's colourful long-tailed birds, a species of parrot.
Presidential security sought help from zoo keepers to capture two birds perched on a tree-top at Rock House area, about four kms away from President's House, officials said.
The other two macaws were found by locals who handed them over to the police.
"The birds are in good health despite being away from the aviary for four days," a spokesman said.
The macaws escaped from the Rajapaksa's residence - commonly referred to as Temple Tree's - during the traditional New Year holidays following which Rajapaksa's office released photos of three of them on Wednesday and appealed for help to find them.