Syrian plainclothes security men whisked away the 20-member team, led by Swedish chemical weapons expert Ake Sellstrom, from a crush of waiting reporters and cameramen as they arrived at their five-star hotel in the heart of Damascus.
Deputy Foreign Minister Faisal Mekdad told the Associated Press before their arrival that Syria will "fully cooperate" with the team.
"I assure you, on behalf of the Syrian Arab Republic, that we will fully cooperate with this team and provide it will all information we have and all facilities to reach a rational conclusion," he said.
"Our basic target is for this team to find facts on ground, especially about what happened in (the Aleppo suburb of) Khan al-Assal, because we, as a government, do not know about any other cases other than the case where chemical weapons were used by terrorists there," he said. Syria's government refers to rebels fighting its rule as terrorists.
The U.N. team's mission will be limited to investigating the alleged use of chemical weapons in three areas, in particular the March 19 attack in Khan al-Assal that President Bashar Assad blames on rebels.
The other two sites have been kept secret.
Assad's government and the rebels fighting to topple him each say the other side has used chemical weapons during the 28-month conflict.
Mekdad insisted that Syria "will never use chemical weapons against its people."
"We said that these weapons were used in Syria, and Syria was the first to inform the United Nations that armed groups used these weapons in Khan al-Assal," he said. "We had wished that the United Nations had conducted the investigation immediately at the time so the team would not find difficulties gathering evidence."
In June, Washington said that Syria's government used the nerve agent sarin on two occasions in the embattled city of Aleppo in the March 19 attack on Khan al-Assal and in an April 13 attack on the neighborhood of Sheikh Maqsud.
The letter from then-U.S. Ambassador Susan Rice also said unspecified chemicals, possibly including chemical warfare agents, were used May 14 in an attack on the town of Qasr Abu Samrah and in a May 23 attack on the town of Adra.
In March, Britain and France told the U.N. secretary-general they have reliable evidence that the Syrian government used chemical weapons near Aleppo, in Homs and possibly in Damascus.
The British and French ambassadors told Ban Ki-moon in a letter on March 25 that soil samples and interviews with witnesses and opposition figures backed their belief that the government used chemical shells that had caused injuries and deaths, diplomats and officials said. They spoke on condition of anonymity because the letter has not been made public.
On March 23, Britain and France asked the U.N. chief to investigate allegations of chemical weapons use in two locations in Khan al-Assal and the village of Ataybah in the vicinity of Damascus, all on March 19, as well as in Homs on Dec. 23.
Associated Press Writer Jamal Halaby in Amman, Jordan, contributed reporting.