The UN's World Food Programme was escorting a convoy of trucks taking essentials for hundreds of thousands of people in rebel-held areas on Thursday when it fell victim to a roadside bomb attack, the defence ministry said.
"Reports state the LTTE has also launched an artillery attack at these unarmed lorries," the ministry said, referring to the rebel Liberation Tigers of Tamil Eelam.
No one was hurt and the convoy returned to the government-held town of Vavuniya, the ministry said.
Earlier Thursday, the rebels accused the military of bombing bridges in rebel-held areas in a bid to block food reaching civilians.
Most international aid agencies have quit the troubled region after a government order, leaving only the International Committee of the Red Cross.
The WFP's action was a one-off, and they no longer have a presence in the area.
Meanwhile, the military said it had used jets to bomb an arms store and an LTTE command centre in the north, the ministry said.