A little over an hour into their transatlantic flight, Kate Carson’s daughters had just laid down to sleep when suddenly their Air New Zealand “cuddle class” skycouch became a “nightmare” scene.

A stomach bug that had been troubling their family during the holiday reared its head again: her youngest, three years old, started throwing up. “The first time, she was asleep, and no one saw it coming, and it went all into the seat … down the side and into the crack,” Carson says.

Her daughter did not stop vomiting until an hour before they landed in Los Angeles. “Everyone’s worried about their kid crying on a plane – no, no, no – this is so much worse,” Carson says.

Her husband spent “10 straight hours just trying to catch whatever else she threw up into the barf bag” while Carson cleaned the plane bathroom “top to bottom”. After she’d “nuked” it with what she thought was a cleaning product, supplied by the crew, she realised all she had been given was “deodorising spray”. (When contacted by Guardian Australia, Air New Zealand declined to comment.) Carson and her husband decided to abandon the plan to surprise their daughters with a visit to Disneyland during the layover. Instead, they booked into a hotel to do laundry.

As the other passengers disembarked, ground crew were waiting to take away the family’s chairs, clean around them, then replace them with an entirely new row. “I was so grateful … you come in and you sit on a seat of a plane and you just don’t know who was there, you don’t know what happened,” Carson said.

But some passengers have been left with clues. A Delta passenger sat in the faeces of an ill service animal from the previous flight; a man travelling with Air France found blood and faeces on the floor from a passenger’s hemorrhage two flights before; while Air Canada passengers were threatened with being placed on a no fly list for refusing to sit in vomit-soaked seats. In a statement, Delta said their safety and security protocols are “top customer priorities”; Air Canada said “for any extraordinary situations” the airline “follows the standards as set out by the health authorities to deep clean and disinfect aircraft cabins using professional grade products”; while Air France did not respond to requests for comment.

While these incidents suggest airlines don’t always allow hygiene issues to hinder the schedule, they can also cause major delays. In 2023 a woman’s trail of diarrhoea forced a Delta flight from Atlanta to Barcelona to turn back, while a 2008 flight diverted after several passengers from the same New England tour group were struck with norovirus mid-air – and was the subject of a study by the US Centers for Disease Control and Prevention.

Travel is a major risk factor for gastrointestinal illnesses, with travellers’ diarrhoea thought to affect between 30% and 70% of travellers during a two-week period. Combined with turbulence increasing nausea and logistical barriers sometimes hindering passengers from making it to the lavatory on time, air travel can become not just messy but a biological hazard.

Flights are delayed due to biological hazards from passengers “unfortunately more regularly than you would think”, says Justin Brownjohn, a former operations manager for Singapore Airlines, Qatar Airways and Virgin Australia.

While there is no publicly available data on the subject, and multiple airlines refused the Guardian’s requests for internal data, Brownjohn says that, from his experiences, an airline would probably be delayed due to a biohazard issue roughly once a week.

The extent of the delay depends on what the substance is, “how bad it is”, where it is on the aircraft and where the flight has landed, says Brownjohn, now manager of the Royal Melbourne Institute of Technology’s Aviation Academy.

When an incident happens midflight, cabin crew will attempt to contain the contamination, using biohazard kits they have on board for this purpose, which include an absorbent powder that can turn liquid into clumps so it can be scraped away. Then the area will be sanitised with a spray.

“But depending on the severity of the contamination, the aircraft may need a more thorough cleaning and disinfection by the ground team before it can operate again,” says Leila*, a flight attendant from a low cost carrier airline in the Middle East.

She says that “the really extreme cases”, when body fluids get into carpets, seat cushions or other areas that are difficult to properly clean, can cause a delay. Sometimes whole sections of carpet have to be removed.

Flight attendants may also be able to swap out seat covers, block off a row of seats if the flight isn’t full, or close off a bathroom, says Seth Heiple, a flight attendant for a major US carrier and a safety representative for the Association of Flight Attendants. “Unfortunately, we’ve had faeces all over the walls of a lavatory.”

Flight attendants will notify the pilot, who will warn the ground crew, or other teams who may need to be involved, such as maintenance crews if seatbelts need to be replaced due to contamination, Heiple says.

Most airlines have third-party contractors who provide the ground crew cleaning services. Osman Yılmaz is the managing director of one such service, Çelebi Aviation, which contracts for airlines including Lufthansa, Emirates and Air China at their stations across five countries.

Yilmaz says crews are “well trained” in cleaning up vomit and spills. “But something beyond that, they don’t have to touch it.”

For more extreme cases, especially if there is blood, specialist cleaning companies with training in biological messes are called in. These experts can usually resolve issues fairly quickly in major ports, Brownjohn says.

However, when incidents occur in smaller airports without access to cleaning and engineering support, “the airline quickly runs out of options about what they can do”, Brownjohn says.

“It’s usually one of two: do the best they can – by cordoning off areas, changing seat covers, using air freshener – the other option is usually cancel the flight,” he says.

Heiple says in these situations “if the smell’s really bad, they might be legal to fly, but it’s not something that we want to accept if it’s going to maybe trigger more people to throw up on the next flight”.

The captain has the final authority on whether to accept an aircraft, Heiple says, but the crew will occasionally demand additional cleaning through a consultative process.

These kinds of delays are becoming more common with the advent of low cost carriers who turn planes around in short windows. “The system is not designed to accommodate last-minute problems like this,” says William McGee, who previously worked in airline operations management.

Last century, aircraft spent more time on the ground between flights, while airlines had a much lower rate of seat occupancy (about six in 10) and in-house cleaning staff. This meant “they had more ability to address this stuff”, says McGee, now a senior fellow for aviation at the American Economic Liberties Project.

While long-haul international flights are generally cleaned between flights – because these are the routes that make the most money – domestic short haul routes are often only thoroughly cleaned at the end of the day, McGee says.

Aircraft are typically deep cleaned every two weeks or so – which involves cleaning nooks and crannies and steaming carpets and seats, Brownjohn says.

McGee says: “My best advice is take the first flight of the day because chances are that’s the cleanest that plane is going to be all day.”

Heiple agrees. “Between flights during the day, [a passenger] might not realise that somebody used the tray table to change their baby and now it’s contaminated.

“Anything that can come out of the human body has and does on the aircraft unfortunately.”