However the airline failed to mention the person suffering the medical emergency was at the controls of the plane, and that the diversion was handled by a pilot who just happened to be onboard.
"We had no idea whatsoever what the incident was," said a passenger identified as Sheila, 69, talking to the BBC.
"It could have been medical, a fire, mechanical problems. Everyone was really concerned."
Sheila said they were only really aware of the situation after they had landed in Porto, and the pilot had to be carried down the steps. Cabin crew reportedly said he had begun drifting "in and out of consciousness" at the controls.
"They made the announcement that there had been an incident on the flight deck and another Jet2 pilot who happened to be on holiday came forward from the back of the plane," another passenger, Nichola Banks, told the MailOnline.
An off-duty pilot was found among the passengers and he offered his services to the cockpit, where he "didn't come out until he helped the pilot off the plane when we landed," said Banks.
The off-duty pilot for Jet2 had been going on holiday to Madeira at the time.
Jet2 informed the MailOnline that it was the first officer and co-pilot that landed the plane, "as it should have been."
However, he would have been grateful for the assistance.
"The crew did a great job. I was quite relaxed because of the spare pilot and that there was a co-pilot," said passenger Banks.
Passengers described the "hushed silence while the plane started its descent," the long wait for further information and how crew member was waiting with a wheelchair by the cabin door.
After the pilot reportedly took ill, the plane's first officer successfully diverted the plane and made the emergency landing, a spokesman for Jet2 told Business Insider.
Shortly after the incident the airline tweeted a statement: "We would like to apologise to customers travelling on #LS765 from #Manchester to Funchal, #Madeira which has diverted into Porto, #Portugal due to an onboard medical situation. We are working to get you on your way ASAP. Please see our agents 'Portway' at Gate 2 for more info. Tx"
A spokesman for Jet2 said: "Flight LS765 from Manchester to Funchal diverted to Porto as a precautionary measure this morning, due to one of the pilots feeling unwell.
"A standby aircraft and replacement crew will be flown to Porto so that we can get customers on their way to Funchal as soon as possible."