The Liberation Tigers of Tamil Eelam (LTTE) hit two military installations in the Weli Oya region, where security forces launched a new drive against the rebels on Saturday, a top security source said.
"They dropped three bombs at two locations and flew back," the source said.
"The damage caused is insignificant, but the attack is symbolic. It shows they have coordinates of military installations.
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One soldier was injured in the attacks, the source said.
The Czech-built Zlin-143 aircraft managed to withdraw unchallenged despite new anti-aircraft defences set up by the military in the island's northern and eastern regions, the sources said.
Hours earlier, the military had used jet aircraft to bomb suspected Tiger artillery positions in the same region, the defence ministry said.
The pre-dawn Tiger air raid on Sunday was the rebels' fifth aerial strike since they launched an air wing in March 2007.
Their first attack was against an airbase that shares a runway with the count