Liam Corcoran, who ran away from home, got through a security screen by mingling with families going through Terminal 1 of Manchester Airport yesterday afternoon.
The boy was discovered by co-passengers while the Jet2 flight LS791 to Rome was in mid-air.
Manchester airport and Jet2.Com have launched a full-scale investigation into how the boy managed to evade so many checks and end up in Italy. It is understood five members of staff working for Jet2.Com have been suspended from duty while the investigation takes place.
UK transport secretary Justine Greening said the incident was "incredibly concerning".
"I treat security breaches very, very seriously indeed, so we are now reviewing urgently with Manchester Airport, and indeed the airline, exactly what happened," Greening said.
The boy went straight to the nearest aircraft that was boarding - the flight to Rome - where he was also missed during a head-count on board the plane.
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"He got himself to the airport. It looks like he evaded some passport checks and some boarding pass checks and ended up in Rome," airport spokesman John Greenway said.
A spokesperson for Jet2.Com said: "On Tuesday an 11- year-old boy cleared security at Manchester Airport, without the necessary paperwork but had been through a full security search.
"We have launched a full investigation into what is a serious incident, and the staff involved have been suspended pending the outcome.
"The boy has been returned safely to his family."
The boy was reported missing yesterday after his mother lost track of him at a shopping center in Wythenshawe, close to Manchester airport, police said.
"He had run off from his mum," Greenway said.
The boy stayed on board the plane when it landed at Rome Fiumicino Airport and was flown back to Manchester when the plane returned on Tuesday evening.
Greater Manchester Police said no crime had been committed.
The incident comes as some two million people head to Britain for the Olympic Games, which open here on Friday.
Security at the Games has been under the spotlight after Britain was forced to deploy an extra 4,700 troops to guard venues after the private security contractor said it could not supply enough guards for the high-profile event.