Airport officials have said they had no objections to soldiers returning from Afghanistan wearing their uniforms in the terminal building.
Up to 200 had to put on civilian clothes at Birmingham International Airport after being told they could not go into the terminal in combat gear.
The airport said it was not involved and believes the order came from a commanding officer.
A flight to RAF Brize Norton in Oxfordshire was diverted to Birmingham.
The soldiers, who were travelling back to spend Christmas with their families, had their journey changed because of bad weather.
On their arrival they were asked to reclaim their baggage from the runway and change out of their kit.
Most opted to change on the tarmac rather than re-board the plane.
Joe Kelly, acting managing director of Birmingham International Airport, said no instruction was given by an airport employee.
He said: "We believe that the instruction was given by the commanding officer and we have since intervened to try to ensure this does not happen again at Birmingham International Airport.
"However, we have to recognise that the soldiers remain at all times under the control of their commanding officer and the MoD is currently investigating why this incident has occurred."
The Ministry of Defence said it was aware of the incident but did not have any further details.
A spokesman said the order was likely to have been issued by the commanding officer on security grounds.
He said: "For security reasons, the MoD wishes to reduce the military profile on flights carried out on its behalf at civilian airports."