Airstrikes were carried out by Kfir and MiG-27 aircraft Monday on the base in Thoppigala, said air force Captain Ajantha Silva.
The rebels - formally known as the Liberation Tigers of Tamil Eelam - confirmed the air raid, but denied any casualties were sustained.
"Yes, there was some air movement and some sort of bombing, but we suffered no casualties. The report is negative," spokesman Rasiah Ilanthirayan said from Kilinochchi, the de-facto rebel capital in the north.
The Thoppigala camp serves as a major training base for the rebels. It is considered one of the last major LTTE redoubts in the east, as Sri Lankan forces have carried out several ground and air attacks over the past year and captured territory, the AP said.
The rebels have been fighting since 1983 to create a separate state for ethnic minority Tamils in the north and northeast, following decades of discrimination by the Sinhalese majority.
About 65,000 people died in the conflict before the government and rebels signed a Norwegian-brokered cease-fire in 2002.
Renewed fighting has killed about 4,000 people since the truce faltered in late 2005, European monitors say.
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