Military sources said six aircraft were deployed for the bombing raid based on intelligence reports that Prabhakaran was receiving medical treatment at a jungle hideout in the region.
The LTTE denied the attack saying the military had attacked a civilian target.
The group released pictures of the Tiger leader at meetings with his fighters.
The latest air attack came as the defence ministry said two suspected rebels were shot dead in skirmishes just outside LTTE-controlled territory on Tuesday.
Since the start of this month, Sri Lanka's defence ministry has said government forces have killed 594 rebels while 26 soldiers have died.
The military's claims cannot be independently verified as journalists and human rights workers are not allowed access to the region.
The bombing raid came a day after Mahinda Rajapakse, the Sri Lankan president, defended his decision to formally withdraw from a 2002 ceasfire with the LTTE .
Rajapakse also stated that he did not believe in a military solution to the decades-old Tamil separatist campaign.
But he said he would not negotiate with the LTTE until they stopped their armed struggle.
Thousands of people have died since the Tamil Tigers began their insurgency in the early eighties.