The incident was triggered when a woman entered the security area unchecked, causing police to completely close Terminal 2.
After a weekend of chaos, Munich Airport is back to normal operation, but with delays.
An hour-long blockage of two departure halls caused big problems at the beginning of the holiday in Bavaria.
About 330 flights were cancelled and some 32,000 passengers were affected, as a spokesman for Munich Airport said in a statement on Sunday.
With re booking at this time of year difficult, some 2,000 people spent the night on benches or cots at the airport, according to airline, Lufthansa. Hundreds more were housed in hotels.
Airport representatives and authorities are investigating the safety glitch.
The incident was triggered at a security check on Saturday morning: an unknown woman had passed it without being checked.
As a result, the Federal Police cleared the Terminal 2 and the associated so-called satellite terminal.
It's thought the woman didn't act deliberately. A representative of the government of Upper Bavaria has blamed the incident on an individual failure of the security staff.
Neither the airport nor the mainly affected airline Lufthansa was able to provide information.
The economic damage for mainly affected airline Lufthansa and the airport is expected to reach into the millions.