In a report published Sunday, Pyongyang's state-run Korean Central News Agency (KCNA) accused US Department of Homeland Security officers and airport police of taking a diplomatic package away from the delegation, which it said carried a valid diplomatic courier certificate.
KCNA called the incident "an illegal and heinous act of provocation," adding that US authorities behaved like "gangsters."
The US Department of Homeland Security confirmed that a group of three North Koreans was confronted at JFK, but said they did not hold diplomatic status.
"According to the US State Department, the North Korean citizens were not accredited members of North Korea's Mission to the UN and had no entitlement to diplomatic immunity. The package in question had no diplomatic protection from inspection," a Homeland Security statement said.
"DHS seized multiple media items and packages from the individuals, at which time the North Koreans attempted to physically retrieve the items but were prevented from doing so by DHS officers. The reported aggression was initiated by the North Koreans," the statement continued.
According the 1961 Vienna Convention, diplomatic couriers "shall not be liable to any form of arrest or detention" and the diplomatic bags they carry may not be opened or detained.
The convention also says any person claiming courier status must carry proper accreditation and any courier bags they carry must be visibly marked as such.
The North Koreans were not held by US authorities but refused to board their flight out of JFK, the DHS statement said.
The incident comes as US-North Korea tensions have spiked over Pyongyang's pursuit of nuclear weapons and numerous missile tests this year.
The US has responded with military shows of force in waters around the Korean Peninsula.
KCNA said North Korea regarded the JFK incident as just the latest example of US hostility towards it.
"This mugging act of the US serves as a graphic account telling the world how reckless and despicable the US hostile policy towards (North Korea) has become," the KCNA report said.
"The US should reflect on its reckless act and be fully aware of the grave consequences to follow," it said.
The incident also comes just days after North Korea released US detainee Otto Warmbier
after 17 months in detention. He was sentenced last year to 15 years hard labor on charges that he tried to steal a banner with a political slogan from his hotel in Pyongyang.
On his return to the US last week, doctors said the 22-year-old former student was in a "vegetative state."
North Korea said he had contracted botulism before slipping into a coma, but US doctors said there was no evidence of that.
The North Koreans were in New York to attend a three-day UN conference on rights of people with disabilities. That meeting ended Thursday.