Passengers have described “bedlam” at UK airport check-ins after a global IT outage on what was due to be the busiest day for flying since the start of the Covid pandemic, while train networks have also been disrupted.

More than 5,000 flights have been cancelled worldwide after Microsoft Windows operating systems used by airlines, airports and some air traffic systems were affected.

Several US carriers, including American Airlines and Delta, temporarily grounded all flights. The Dutch airline KLM said flight handling was “impossible” and it would largely suspend operations on Friday morning, while Swiss air traffic had to cut flights by 30%. Problems were also reported in India, Japan and Australia.

In the UK, Gatwick and Luton were among the hubs where airline check-in systems were hit, while the biggest commuter rail network, GTR, said its Thameslink and Southern trains were disrupted due to communications systems failing.

The transport secretary, Louise Haigh, said her department was “working at pace with industry and across government on the issue”.

A passenger at Gatwick, the UK’s second busiest airport, said he had queued for more than three and a half hours at check-in, with staff handing out water to those waiting on what was expected to be the UK’s hottest day of the year so far.

Dean Seddon, 42, from Plymouth, told the PA news agency he had queued since 6am for a flight to Miami with Norse Atlantic Airways. “There are just people everywhere, there must be 400 people in this queue for the check-in desk I’m at … it’s just bedlam,” he said. “[Staff are] doing the best they can but they don’t actually know when it’s going to be fixed.”

The outage hit after the first wave of UK morning flight departures had checked in, sparing some from the worst of the disruption.

The budget airlines Ryanair and easyJet said the situation was out of their control and advised passengers to arrive at airports early, with some flights switching to manual check-in and handwritten boarding passes. EasyJet said customers should expect longer airport queues and advised those travelling from Spanish airports, in particular, to arrive three hours before their flight.

Wizz Air said its website, online check-in and apps were all affected and passengers would need to check in manually.

British Airways said some of its flights were “likely to experience disruption” as the outage had “caused issues across our operational systems”.

There were long queues at Luton airport, while Edinburgh airport said waiting times were extended. Heathrow said the outage was “impacting select systems” but flights were operating and it was “implementing contingency plans to minimise any impact” on journeys.

Ryanair urged passengers whose flights were cancelled to leave airports and use its website or app, once restored, to find options for rebookings or refunds.

Passengers have a right to a refund or to be rerouted, as well as food and drinks during long delays, but are unlikely to be paid compensation for any delays for an incident that will be regarded as out of airlines’ control.

At Palma de Mallorca airport, Jemma Wheeler, 30, told the BBC that her family of five had been standing in a queue for three hours. “We only came for a five-night short break. We thought it was a quick two-hour flight and we would be back in no time to enjoy the nice weather at home,” she said.

Clive Wratten, the chief executive of the Business Travel Association, said the IT issues were having a significant impact on global travel. “Our travel management companies are working flat out to find new arrangements and reassure passengers stuck around the world,” he said.

The analytics firm Cirium said 5,078 flights had been cancelled globally by 3pm UK time. More than 3,200 departures from the UK had been scheduled for Friday, the busiest day since 2019.

The UK air traffic control provider Nats, which had a major IT failure last summer, said its systems were operating normally.

On the trains, the National Rail site said there were “widespread IT issues across the entire network”. It said: “Some train operators are unable to access driver diagrams at certain locations, leading to potential short-notice train cancellations. Other key systems, including real-time customer information platforms, are also affected.”

A spokesperson for the Rail Delivery Group said: “Most trains are still running across the country and rail staff will be able to provide the latest information to customers in person.”

South Western Railway said all its ticket vending machines had stopped working because of IT problelms. Among other operators affected were West Midlands Trains, Avanti West Coast, Great Western Railway and TransPennine Express.

Network Rail, which manages the railway infrastructure, was unaffected.