Sri Lankan jets bombed a suburb of the Tamil Tiger's northern political capital on Tuesday at what the military said was an insurgent training site.
Both the military and the rebels said that casualties or damage assessments were not yet available.
A Tamil Tiger military spokesman said the attack was near the rebel headquarters of Kilinochchi, 330 kilometres (205 miles) north of Colombo, and that it was unprovoked and caused panic among the civilians.
"We don't have details of the locations that were hit," spokesman Rasiah Ilanthiriyan said by telephone. "School children in Kilinochchi panicked and fled from their classrooms when they heard the aircraft."
The defence ministry confirmed that the airforce had carried out bombing sorties over rebel-held territory and said a training base of the "Sea Tigers" was attacked.
"These targets had been previously identified as training bases of the Sea Tigers and had been used as launching pads to attack (the) navy and ground forces in the east during the recent past," the ministry said in a statement.
It said the attack caused "severe damages" to the Tigers.
The Liberation Tigers of Tamil Eelam (LTTE) and the Sri Lankan government have escalated fighting in the past year in tit-for-tat battles that have claimed thousands of lives despite a 2002 cease-fire agreement.
The bitter ethnic conflict has claimed at least 60,000 lives since it began in 1972.