The alert came just a day after the Brussels terror attacks at the city's airport and Metro stations and with France on high alert over the ongoing terrorist threat.
At around 7am, as passengers gathered in the departure areas, they were suddenly told to evacuate the building due to a security alert.
They were forced to gather outside the terminal on the road as they waited for the all clear. Images posted on Twitter showed passengers waiting patiently outside.
Checked in at Toulouse airport, sitting at the departure gate and we've now all been asked to leave. Everyone outside now- Mark Davidson (@vintageMD) March 23, 2016
The reason for the alert was the presence of suspect baggage.
A spokesman for the airport told The Local that the alert was over at around 8.20 and passengers were allowed to return to the terminal.
However the spokesman warned that flights would begin again progressively and that passengers could expect delays.
Belgian investigators revealed on Tuesday that the attackers who targeted the airport hid their bombs in suitcases.
France has stepped up security in the light of the Brussels attacks with 1,600 extra police deployed, mainly to transport hubs like airports.
Members of the public with a ticket fro travel or valid ID will also barred from public areas of airports and rail stations.
Yesterday airport authorities in Toulouse announced that security had been stepped up both in the departure building and on the runways.
Following the Brussels bombings on Tuesday Gare du Nord in Paris was partly evacuated twice over suspect packages. Both proved to be false alarms but showed authorities are not willing to take any chances.
Toulouse airport hit the headlines recently after a British passenger sparked a security alert when he boarded an easyJet flight carrying a small knife.
The passenger made it past security checks but was then kicked off the flight after passengers refused to fly with him on board.