The rebel Liberation Tigers of Tamil Eelam (LTTE) had cleared a jungle patch just north of the district of Trincomalee and were building an airfield when the planes carried out the attack, the ministry said in a statement.
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"The operation was conducted to prevent the construction of this unauthorised air facility, which poses a grave security threat not only to the sovereignty of Sri Lanka but the entire region," the statement said.
The bombardment was the second against the LTTE in two days.
"The bombing raids were over the northeastern region," a military official said, adding that three jets were used in the offensive just north of the same area where warplanes staged three similar sorties Wednesday.
Kfir jets pounded suspected rebel bases Wednesday at Maavilaru and Hirugalaru in northeastern Trincomalee district where the army said the separatists had blocked an irrigation canal.
The LTTE said that the military had carried out two days of bombings in which two civilians