"The first vehicle of the Chemical Weapons Investigation Team was deliberately shot at multiple times by unidentified snipers in the buffer zone area," a statement from the secretary general's spokesperson said.
"As the car was no longer serviceable, the Team returned safely back to the Government check-point. The Team will return to the area after replacing the vehicle."
The UN statement reiterated the need for "all sides" to co-operate fully so the investigators can collect evidence safely.
Syrian President Bashar al-Assad had earlier pledged that a ceasefire would be put in place while the investigators continue their work. He has denied that his troops ever used chemical weapons during the fighting in a rebel-held suburb near the capital, Damascus.
Intimidation tactics are nothing new to UN weapons investigators in a foreign land, according to former UN arms investigator Tim Trevan.
"Clearly this is intimidation against the team," Trevan told CBC News from Washington. "It's something teams have to deal with, confrontation situations like this one."
Trevan added that although it's difficult to say whether the sniper was with the opposition or government forces, "the suspicion must be that this is the Syrian regime."
"They want to show the international community they're willing to go ahead and co-operate, and at the same time ensure it doesn't happen by subjecting the convoy to fire, making the inspection site itself too dangerous to visit," Trevan said.
The United States strongly suspects that Assad's regime was behind the Aug. 21 attack on the eastern outskirts of Damascus. That suspicion is supported by the international aid group Doctors Without Borders, which reported that 355 people were killed in an artillery attack that also included the purported use of a toxic chemical weapon.
The organization's president, Mego Terzian, has said the group is "100 per cent" certain that some sort of neurotoxic gas was deployed.
Its numbers are also consistent with those of Syrian activists and opposition leaders, who have said that between 322 and 1,300 people were killed in the alleged chemical attack.
'Too late to be credible'
Mohammed Abdullah, an activist in the eastern suburb of Saqba, said the UN was expected to visit the rebel-held area on Monday and that the weapons investigators would be under the protection of the Islam Brigade, which has thousands of fighters in the area.
Although Syria has said that a UN team was welcome to visit the site, a senior White House official dismissed the deal with inspectors as "too late to be credible."
British Foreign Secretary William Hague added that it was likely that artillery fire at the site would have destroyed much of the evidence.
Meanwhile, a defiant Assad claimed foreign leaders were making excuses so they could intervene militarily in Syria, telling a Russian newspaper the accusations that his troops used chemical weapons were "politically motivated."
"This is nonsense," Assad was quoted as saying in the interview with Russia's Izvestia daily. "First they level the accusations, and only then they start collecting evidence."
Assad said attacking such an area with chemical weapons would not make sense for the government as there was no clear front line between regime and rebel forces.
Assad says inspections 'politically motivated'
"How can the government use chemical weapons, or any other weapons of mass destruction, in an area where its troops are situated?" he said. "This is not logical. That's why these accusations are politically motivated, and a recent string of victories of the government forces is the reason for it."
Conclusions drawn by the UN team could have a dramatic impact on the trajectory of Syria' civil war, as France, Britain, Israel and some U.S. congressmen urge swift military action against Assad's regime.
French Foreign Minister Laurent Fabius said no decision had been made on a military intervention but that any response would be "proportionate."
"It will be negotiated in coming days," Fabius told Europe 1 radio on Monday. He said that the lack of a UN blessing was problematic, but that all options remain on the table.
"The only option that I can't imagine would be to do nothing," Fabius said.
Meanwhile, the German government is suggesting for the first time that it would support an international military response against Syria if it is confirmed Assad's troops attacked opponents with chemical weapons.
Chancellor Angela Merkel's spokesman Steffen Seibert said Monday that if UN inspectors confirm the use of chemical weapons, "it must be punished."
Russia, who has been a staunch ally of Syria, said last week that the accusations against Assad could be a bid to get the Security Council to stand by the opposition and to undermine efforts to resolve the conflict by convening a peace conference in Geneva.