The UN chief said on Thursday the investigation would look into "the specific incident brought to my attention by the Syrian government".
"I have decided to conduct a United Nations investigation into the possible use of chemical weapons in Syria," Ban told reporters.
Al Jazeera's James Bays, reporting from New York, said: "It will take some time for the UN to get investigators on the ground.
"They need to get assurances from the government and the opposition that their investigation team will be safe when they are on the ground carrying out their work."
Syria's government and rebels on Wednesday demanded an international inquiry into the deadly attack which both sides cite as an evidence that the other has used chemical weapons.
The opposition Syrian National Coalition said it also wanted an investigation into another incident of alleged chemical attack in Otaiba, a town near the capital city of Damascus.
Ban said he was aware of other allegations of the reported use of chemical weapons, but did not make clear whether those would be part of the investigation.
"Full cooperation from all parties will be essential. I stress that this includes unfettered access," the UN chief said.
The Organisation for the Prohibition of Chemical Weapons and World Health Organisation are helping to set up what the UN chief predicted would be "a difficult mission".
Bays said: "Some countries, notably Britain and France, wanted a wide-ranging investigation into all the allegations.
"Russia though said they were asking into investigations into some incidents which were merely, in the words of the Russian UN ambassador, 'rumours'."
The attack, which killed at least 26 people on Tuesday, if confirmed, would be the first use of chemical weapons in the nearly two-year-old conflict.
Washington has disputed the regime's claim and said there was no evidence that the rebels had fired chemical weapons.
"So far we have no evidence to substantiate the reports that chemical weapons were used [on Tuesday]," said Robert Ford, the US ambassador to Syria, adding that the administration was extremely concerned and trying to verify reports of such weapons being used.
Al Jazeera And Agencies