The LTTE alleged that five people were killed and one person was seriously wounded when the Sri Lankan Air Force (SLAF) dropped bombs barely 500 metres from the New General Hospital in Kilinochchi on Thursday.
But the Sri Lankan government said that the attack was on a rebel "military training base south-east of Kilinochchi."
Kilinochchi, in the northern region of Wanni, is the political headquarters of the LTTE.
The pro-rebel Tamilnet website said that at least three bombs were dropped by two Kfir fighter-bombers at about 2.00 pm on the new hospital at Anandapuram located on the A9 highway linking Vavuniya with Jaffna.
The bombs shattered windowpanes and brought ceiling fans crashing down on patients who were having lunch in the wards. The dead were members of a single family.
At least five hundred patients fled from the hospital as the bombs fell.
Military base says government
But the Sri Lankan government's National Security website said that the target was a "military training base".
The Air Force had undertaken "well planned" missions aimed at neutralising identified LTTE targets at Mannar and Kilinochchi to "pre-empt" efforts by the rebels to launch a major military offensive, it maintained.
"The target details were confirmed by both ground and electronic intelligence."
Fear of LTTE offensive in East
The LTTE had been preparing for a major offensive in the eastern district of Batticaloa, the National Security website said.
Tamil civilians, who were fleeing areas under the control of the LTTE and moving into government-held areas in Batticaloa, were saying that the militants were preparing for a major offensive, it said.
The firing of artillery and mortars on the army detachments in Kadjuwatte and Mankerni on the eastern coastal road, and retaliation by government troops, had triggered the migration of hundreds of Tamils in panic.
The shelling had taken place over October 31 and November 1.
The government further said that 189 Tamils had fled the LTTE-held Kaddimurichchikulam and Kirimichchai area. Over 150 had moved to the government-held Punani, and 33 to Mankerni.