But Stephane Dujarric told reporters the incident has nothing to do with the quality of humanitarian aid now going through U.N. channels into Syria.
A physician who administered the vaccinations in rebel-held parts of northwestern Syria told The Associated Press in mid-September that at least 15 children, some of them just babies, died. The physician, Abdullah Ajaj, said the children exhibited signs of "severe allergic shock," with many suffocating to death as their bodies swelled.
Syria's ambassador to the United Nations has demanded a U.N. investigation into whoever is responsible. In a letter to U.N. Secretary-General Ban Ki-moon and the president of the Security Council last month, Bashar Ja'afari called the deaths a "crime against humanity."
"What happened with the vaccines was a real tragedy, but it was basic human error," Dujarric said.
The World Health Organization last month said the muscle relaxant had been kept in the same refrigerator as a substance meant to dilute the measles vaccine. It said the exact person or group responsible for the laboratory was not known.
Dujarric on Wednesday did not name the NGO partner and referred to the WHO report.
Syria's conflict between the government and rebel groups, now in its fourth year, has caused the collapse of its health system in contested areas. Nationwide vaccination efforts have been thrown into disarray, and polio re-emerged in parts of Syria last year.
After the children's deaths, the Western-backed opposition based in Turkey said it had suspended the second round of measles vaccinations. The campaign was meant to target 60,000 children.
The United Nations and the international community have struggled to reach civilians inside Syria with humanitarian aid. In July, the Security Council unanimously approved aid delivery through four border crossings with Turkey, Jordan and Iraq without the approval of the Syrian government, which humanitarian chief Valerie Amos has blamed repeatedly for slowing the aid process.
The Syrian ambassador in his letter demanded that the U.N. inform his government before delivering aid through those crossings.
Dujarric defended the quality of the aid the U.N. is facilitating into Syria, saying it has "seen no evidence of tainted food or medicine that is old or tainted coming through U.N. channels."
The U.N. says more than 190,000 people have been killed since the start of Syria's uprising against President Bashar Assad in March 2011.