Although the problem is now fixed, the temporary breakdown meant for a time on Wednesday morning all passengers had to be checked in manually.
The situation caused “chaos” at the airport, one passenger told daily 20 Minuten, with long queues backing up at the check-in desks.
Some expressed their frustration on twitter, while airlines apologized to customers.
An airport spokesman told the paper that the breakdown was due to an electricity failure during the night, but that the issue affecting the check-in system was now fixed.
However queues of up to 40 minutes are still possible at the airport, which is the main hub for Swiss International Airlines.
“We recommend that travellers who have to fly from Kloten allow more time,” said the spokesman.