The US government shutdown is creating havoc at New York’s major domestic airport at the busiest time of the week.

The Federal Aviation Administration (FAA), which runs air-traffic control, is delaying arrivals at La Guardia airport, the closest to Manhattan, due to “staffing issues”.

It says: “There is a Traffic Management Program in effect for traffic arriving La Guardia Airport, New York, NY (LGA). This is causing some arriving flights to be delayed an average of 1 hour 26 minutes.”

The staff shortages are at remote Air Route Traffic Control Centers in Washington DC and Jacksonville, Florida.

The FAA tweeted: “We have experienced a slight increase in sick leave at two facilities. We are mitigating the impact by augmenting staffing, rerouting traffic and increasing spacing between aircraft when needed.”

The warning applies until 9pm local time on Friday.

Delays are building rapidly. More than 200 inbound flights are currently showing as significantly behind schedule. Arrivals from Pittsburgh, Knoxville, Cleveland, Fort Myers and Chicago are delayed by three hours or more.

The airport said: “There are major delays at LGA. Confirm your flight with your airline.”

Delta Airlines said: “The La Guardia situation is very fluid. With the government shutdown, we have no if or when this will be resolved.

“The status of the situation changes by the minute.”

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It has cancelled round-trips from Raleigh/Durham, Columbus and Louisville, while Air Canada has grounded services from Montreal and Toronto.

American Airlines has cancelled a flight to Boston, while the Southwest departure to St Louis has also been grounded.

Departures are facing delays of up to 20 minutes at present, though that is certain to increase as inbound aircraft are late arriving.

Globally, New York is second only to London in the density – and complexity – of air traffic.

While La Guardia has fewer flights than New York’s international airports, Newark and JFK, it is preferred by many passengers – especially business travellers – for its proximity to Manhattan. International flights from Canadian airports with US pre-clearance are also permitted.

The FAA is now warning that the world's busiest airport, Atlanta Hartsfield, is experiencing departure delays of more than an hour. Gate hold and taxi delays are running at up to 75 minutes.

There are also reports of problems affecting the airports at Newark, Washington National, Tampa and Philadelphia.

Affected passengers will have to fend for themselves until the airline can fly them to their destination. In the US, unlike Europe, there is no obligation for airlines to provide a “duty of care” for passengers if the cause of delay or cancellation is beyond the airline’s control – which staff shortage related to the US government shutdown certainly is.

As federal employees, air-traffic controllers have missed two successive monthly pay days due to the partial shutdown.

On Thursday the FAA tweeted a message of reassurance about safety. But on the same day, executives from the big US airlines warned that the aviation system was at a “tipping point”.

Robin Hayes, chief executive of New York-based jetBlue, said: “The longer this goes on, the longer it will take for the nation’s air travel infrastructure to rebound.”