"We have at Lufthansa a reporting system where crew can report without being punished their own problems or they can report about problems of others without any kind of punishment. That hasn't been used either in this case, so all these safety nets we are so proud of here have not worked in this case," Spohr said.
Lubitz had been with Germanwings since September 2013 and had completed 630 hours of flight time after training at the airline's flight center in Bremen, Germany, the company has said. Germanwings is the budget carrier for Lufthansa.
The CEO said he didn't know much more than what has been released by French authorities: The captain left the cockpit, tried to regain access by knocking on the door and "the door was either kept locked or not opened in the way it was supposed to be, and that for sure is a clear indication that the remaining pilot -- the co-pilot -- didn't want the captain to return."
Had the copilot suffered a medical emergency -- as some experts speculated in the initial hours after the accident -- there are safety procedures in place so that the pilot can re-access the cockpit, he said. That is, "unless the person on the inside locks it and this apparently has happened here," the CEO said.
After the September 11, 2001, attacks, cockpit doors were manufactured to withstand manual force and small weapons, so there was "no way to get back to the cockpit for the captain," he said.
Spohr was asked why Lubitz was allowed to be alone in the cockpit. American airlines require that any pilot leaving the flight deck be replaced by a flight attendant, so that two people remain in the cockpit at all times, but that's not the case with all airlines internationally, CNN aviation analyst David Soucie said.
A Lufthansa spokesman previously said that the airline complies with all German and European aviation regulations, something Spohr reiterated in his CNN interview.
"Most airlines around the world follow the same procedures as Lufthansa that in flight phases with low workload, the pilot can leave the cockpit -- especially for physical need -- and then he returns to the cockpit as fast as he can. That's a global thing, most accepted procedure, which we have used at Lufthansa for many, many years," Spohr said.
Asked if the airline might reconsider this policy in light of Tuesday's crash, Spohr said it was possible.
"I think we look at that as well, but we should not put the whole system at stake just because of this terrible single accident," he said.
The airline will be consulting with its own experts, aviation authorities and experts with other airlines to determine what, if any, of its procedures need to be bolstered to prevent future such accidents from occurring, Spohr said, adding that he stood strongly by the manner in which Lufthansa operates airplanes and trains its employees.
"We understand emotions after this terrible accident, but for us as professionals we need to ensure the safety focus of Lufthansa is in no way touched -- and I promise you it's not -- and we will do our very, very best to even improve it further."