The attack came after a weekend of heavy shelling that killed more than 300 people and injured more than 1,000 civilians in what the UN has described as a "bloodbath".
Many of the casualties from that fighting had been taken to the Mullivaikal hospital.
The UN estimates that about 50,000 civilians are still trapped in the narrow strip of land held by the separatist LTTE, commonly known as the Tamil Tigers.
The government has repeatedly denied shelling the war zone, saying it is the separatists who are attacking civilians.
Seevaratnam Puleedevan, a Tamil Tiger spokesman, said civilians were fleeing in all directions inside the zone.
"There's no place to seek shelter or protect themselves," he said.
"We are really afraid that if the Sri Lankan government is not being pressured to stop the carnage, then many more civilians will die."
Keheliya Rambukwella, the Sri Lankan defence spokesman, denied the army had launched any air raids or used artillery.UN 'appalled'
Ban Ki-moon, the United Nations secretary-general, said on Monday that he was "appalled at the killings of hundreds of civilians in Sri Lanka over the weekend".
In a statement, Ban repeated his call for both parties to cease using heavy weapons and accused the Tigers of "reckless disrespect'' for the safety of civilians.
Human rights groups suggest the Tamil Tigers are using civilians as human shields.
In recent weeks, the fighting has forced tens of thousands of people to flee to state-run refugee camps.
The LTTE is believed to be close to defeat in its 26-year battle for a separate homeland in the north and east of the island for the country's minority Tamils.
The government has refused to declare a humanitarian ceasefire saying it would allow the LTTE to regroup.