The Liberation Tigers of Tamil Eelam (LTTE) killed one soldier with a rocket-propelled grenade fired at troops manning a defence line at Nagarkovil on the Jaffna peninsula late Wednesday, the ministry said.
An unidentified gunmen also shot dead a civilian in the northern town of Vavuniya on Wednesday, a day after six people were shot dead in the same area.
The ministry also accused the LTTE of taking over a civilian hospital inside the rebel-held eastern area of Vakarai in order to treat their wounded following heavy fighting with security forces on Tuesday.
The ministry said the Tigers fired 81 mm mortars at troops in the east and security forces retaliated in kind.
There were no immediate reports of casualties on either side in the shelling.
More than 60,000 people have been killed in Sri Lanka's Tamil separatist conflict in the past 35 years.
A truce brokered by peace broker Norway has been in effect since February 2002, but ceasefire monitors say it holds only on paper.