"The hospital building was intact, but we are not sure about any of the equipment," Nanayakkara said.
Last month, about 300 people had to flee the hospital due to fighting and the LTTE, commonly known as the Tamil Tigers, has accused the military of shelling the facility on purpose.
The military denies this and has published aerial photos showing the hospital intact.
Sabarathnam Selvathurai, the head of the LTTE's international financing network, was killed with 16 other separatist fighters on Thursday, according to the military.
"Mortar fire killed the chief of the LTTE's financial wing yesterday," Nanayakkara said.
The fighting occurred in Puthukkudiyiruppu, which is the last town held by the LTTE, which has been pushed back into a section of the northeast of the island over recent months.
The LTTE could not be reached for comment to verify the claims. Journalists are also barred from the conflict zone.
The government said that all of the Tamil Tiger's senior leadership are in the northeastern zone, along with tens of thousands of trapped civilians.
The LTTE has been fighting a secessionist battle for a separate Tamil homeland in the northeast since 1983. Tens of thousands of people have died in the fighting.