The NHS app and website experienced an outage on Wednesday afternoon, with users unable to access their digital COVID vaccine passes, NHS Digital said.
One traveller told Sky News she had missed her flight to France as a result of the app crashing.
An NHS COVID Pass shows proof of a coronavirus vaccination as well as test results.
NHS Digital confirmed the service had been "temporarily unavailable between 11.45am and 3.15pm".
But some panicked NHS app users with imminent travel plans were forced to pay for new flights after being unable to board without proof of vaccination.
Caroline Frost, a journalist and broadcaster, told Sky News she had a choice of paying £420 for an express PCR test and a flight later this evening or £80 to fly out tomorrow.
She was due to fly from Heathrow to Nice on business but has now rebooked to leave on Thursday.
"I had all this previous documentation, but there was nothing they could do," she said.
"There is proof I have been through this many times, I have ticked all the boxes, I don't have COVID, I have a double vaccination test in my hand, I just don't have the app.
"It was a jobsworth moment. She said I sympathise, but there is nothing I can do. She phoned her superior, there was nothing he could do. There we were.
"It was immensely frustrating, and it felt like such a waste of money. And of course, when the app is up and running I am the same person, I'm going to be in the same condition of vaccinated eligibility to travel."
An NHS Digital spokesperson said: "The NHS COVID Pass service was temporarily unavailable between 11:45 and 15:15 today as a result of a technical issue with a global service provider that affected many different organisations.
"Following an urgent investigation, this has been fixed and COVID Passes are available both via the NHS App and online."
People travelling abroad or attending events and venues in England may be asked for proof of their COVID-19 status, which is why instant access to the COVID Pass is important.
Callum Melia, from Liverpool, who is currently on holiday in Naples told Sky News he had been unable to visit a number of museums he had prebooked as he could not prove his vaccination status, costing him around £20.
He said: "We found upon arrival we couldn't access the app and gain entry to the museums.
"This lasted from about 12 - 5.
"We could only gain access to the app once we arrived back at the Airbnb so there was not much else we could do in the meantime."
Earlier this month, Scotland's newly launched vaccine passport app was also hit by technical problems, meaning people are unable to register their details on it.