Officials at Manchester airport and at the airline Jet2.com said Wednesday they were investigating how the boy got aboard the flight to Rome and wasn't detected until the cabin crew identified him during the flight.
"This is an unusual and serious breach and we are keen to find out what has gone on," the government's transport secretary, Justine Greening, said.
The unusual incident took place Tuesday amid heightened security concerns during the run-up to the Olympics.
The Manchester Evening News quoted Sarah Swayne, a passenger on the return flight, as saying the boy didn't seem to be fazed by the fuss he had caused.
"He just sat there chatting away about how he'd been trying to run away from home," Swayne was quoted as saying. "He seemed quite innocent, really, and I don't think it had sunk in how serious the situation was."
An undisclosed number of security staff and airline employees have been suspended following the incident.
"It's not technically a breach of security," airport spokesman Russell Craig told the BBC. "The boy posed no threat to the aircraft. He went through a security process."
Craig said CCTV images showed that the boy mingled with families moving through the airport on a busy day.
In a statement, the airport described the incident as "extremely serious."
"It is clear that documentation has not been checked correctly at security and the boarding gate," the statement said.
Jet2.com said the boy was returned to Manchester and reunited with his family.
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