The UN verification team was visiting former Syrian military and intelligence posts in the Bekaa valley to check whether Syria had completely withdrawn its forces from Lebanon.
While making its inspections, the team drove towards a post manned by the Popular Front for the Liberation of Palestine-General Command (PFLP-GC).
"One man was standing at the entrance of the camp and would not allow the team to enter, and told them that it was a Palestinian camp, not a Syrian post," a security source said on Wednesday.
The PFLP-GC said the team was not allowed into the base because the fighters were not expecting them and were not sure of their identity.
"It was a misunderstanding. Our people were not expecting them and they were taken by surprise," a PFLP-GC official said.
"The fired shots were not directed at the UN team."
The eight-member team, which was accompanied by Lebanese army officers, left without inspecting the border post. But the PFLP-GC said they were welcome to return and inspect the post.
Syria told the UN last week that it had ended its 29-year military presence in Lebanon and was in full compliance with Security Council resolution 1559.
But UN Secretary-General Kofi Annan said he could not confirm the withdrawal until the UN verification mission had completed its checks.