Domestic arrivals and departures continued after the pipe break with delays, and some global flights have been diverted to other terminals.
"We will thoroughly investigate why this pipe burst and thoroughly investigate why it was not adequately protected and thoroughly investigate the contingency plan for this event", Rick Cotton, executive director of the Port Authority of NY and New Jersey which manages the airport, said at a press conference.
The cause of the break appeared to be "weather-related" but would be investigated, as would why the pipe had not been weather protected and whether other failures contributed to the disruption, officials said.
Worldwide arrivals to Terminal 4 were suspended earlier, with passengers who were already arrived being taken to other terminals for processing. The authority said it will "hold those responsible accountable for any shortcomings we find".
Terminal 4 reopened before 8 p.m. on Sunday night, as global arrival "resumed operations".
Meanwhile, Jan Coates told The Independent: "Some of our family are just back from a fabulous holiday in NY over New Year". That meant that all of the flights bound for Kennedy had to divert to other airports or turn around. Video on social media showed water pouring out of the ceiling, eventually leading to the terminal being closed and forcing the Port Authority to divert inbound flights to other terminals for several hours.
According to a witness who spoke with the Daily News, one flight cancellation led to a "near riot" among angry passengers in Terminal 4 on Saturday night - to the point that police had to be called in.
Passengers arriving at the Queens airport said on Twitter they have waited as many as six hours on the tarmac before their plane docked at a gate, then as many as eight hours to collect their baggage from carousels.
Domestic arrivals and departures, and worldwide departures operated with delays.
The extreme cold and recovery from Thursday's snowstorm created a "cascading series of issues for the airlines and terminal operators", the Port Authority said.
"These included frozen equipment breakdowns, difficulties in baggage handling, staff shortages and heavier than typical passenger loads", the statement said. Senator Chuck Schumer said that everything that could go wrong, did go wrong. While numerous bags have been removed from the water, some travelers have said that they have not received any indication of when they'll get their luggage back.
Domestic and global flights are running out of Terminal 4 with delays, as of Monday morning.
And earlier Saturday at JFK, the right wing of a China Southern plane hit the tail of a Kuwait Airways plane, the Port Authority said in a statement.
Sen. Chuck Schumer of NY said JFK officials should have foreseen some of the problems. "I'm exhausted, man", she said, in about the only sentence that could be printed without obscenities.
Worldwide airlines have committed to have baggage reunited by passengers in New York City by Tuesday morning, said Cotton.