Military spokesman Udaya Nanayakkara said they were investigating the blast which was believed to have been caused by a hand grenade.
Eyewitnesses said visitors to the zoo were seen fleeing the area.
The bombing comes as the country prepares to celebrate 60 years of independence from British colonial rule on February 04 and the capital is under a tight security blanket.
Police have blamed Tamil Tiger separatists for earlier bombings which have targeted civilians.