The panel said it has no conclusive evidence about the alleged use of sarin as chemical weapons.
In Washington, White House spokesman Jay Carney said it's highly likely that the Assad regime and not the Syrian opposition was behind any chemical weapons use in Syria.
The dueling statements highlighted the difficulties of investigating allegations of chemical weapons use.
President Barack Obama has said the use of chemical weapons by the regime is a "red line" but he needs more time to determine if Assad's forces had used chemical weapons in the Syria's civil war.
The latest controversy was sparked by Carla Del Ponte, a former war crimes prosecutor.
She told the Italian-language Swiss public broadcaster SRI in an interview late Sunday that her panel's investigators have "strong, concrete suspicions but not yet incontrovertible proof of the use of sarin gas from the way the victims were treated."
"We have evidence on the use of chemical weapons, in particular sarin. Not by the government, but the opposition," Del Ponte said, adding that this was based on interviews with victims, doctors and field hospitals in neighboring countries.
On Monday, the commission said that it "wishes to clarify that it has not reached conclusive findings as to the use of chemical weapons in Syria by any parties to the conflict." As a result, "the commission is not in a position to further comment on the allegations at this time," a statement said.
The four-member panel was appointed by the 47-nation Human Rights Council, the U.N.'s top human rights body, to gather evidence on suspected war crimes and other abuses. It began its investigation in August 2011.
It has had almost no access to Syria, though earlier this year it said it had conducted at least 1,500 interviews and exhaustively corroborated its findings with other sources.
The U.S. has said intelligence indicates Syria has used the nerve agent sarin on at least two occasions, but Obama has stressed that he needs more definitive proof before making a decision about how to respond and whether to take military action.
Fighting in Syria continued unabated on Monday as Assad's warplanes pounded rebel positions inside the Mannagh air base in the north and government troops regained control of six villages along the strategic road that links the northern city of Aleppo with its civilian airport, the country's second largest.
Also Monday, the Britain-based Syrian Observatory posted a video showing several armed men standing in front of wreckage that one of the fighters says is a helicopter shot down late Sunday in the eastern province of Deir el-Zour, along Syria's border with Iraq.
As the man speaks, the camera shifts to a pickup truck piled with bodies. The fighter is then heard saying that all of Assad's troops who were aboard the helicopter were killed in the downing. He says Islamic fighters of the Abu Bakr Saddiq brigade brought down the helicopter as it was taking off from a nearby air base in the provincial capital of Deir el-Zour.
The video was in line with Associated Press reporting in the area. The Observatory, which relies on a network of activists on the ground, said eight troops were killed.
The Syrian government did not comment.
In the past months, rebels have frequently targeted military aircraft and air bases in an attempt to deprive the regime of a key weapon used to target opposition strongholds and reverse rebel gains.
The rebels occupied parts of the Mannagh military air base on Sunday after weeks of fighting with government troops who have been defending the sprawling facility near the border with Turkey for months, the Observatory said. Clashed raged inside the base Monday and the Observatory said both sides suffered casualties in the fighting.
Much of the north has been in rebel hands since opposition fighters launched an offensive in the area last summer, capturing army bases and large swaths of land along the border with Turkey and whole neighborhoods inside Aleppo, Syria's largest city.
The rebels have for months battled regime troops over the airport complex that includes army bases and a military air field.
They've captured village and towns along the strategic highway and earlier this year advanced within a few miles of the airport, cutting the main road the army has been using to ferry troops and supplies to its bases at the airport.
But last month government troops recaptured the village of Aziza on a strategic road that links Aleppo with its airport and military bases, dealing a huge setback to the rebels unable to hold on to the territory in the face of Assad's superior air power.
The state-run news agency SANA reported Monday that "armed forces restored security and stability to [six] villages" south of the city and along the airport highway, calling it a "major strategic victory in the north."
The Syrian conflict started with largely peaceful protests against Assad's regime in March 2011, but eventually turned into a civil war that the U.N. says has killed more than 70,000 people.