Hosting the meeting, France’s Interior Minister Bernard Cazeneuve announced there would be increased identity and baggage controls at stations and more police patrols on board international trains.
The 25-year-old was overpowered by several passengers before he was able to go through with the attack.
El-Khazzani travelled freely on to France, despite being known to French police for his sympathies towards radical Islam.
To counter such people slipping through the net in future, Cazeneuve insisted that information exchanges between members of the EU's Schengen open-bordes zone would be stepped up and made systematic.
Other measures include issuing tickets with passengers' names for long distance travel.
Raffaello Pantucci, a terrorism expert at the Royal United Services Institute in London, says that upgrading security is clearly very important and possible but raises several issues.
"The concern is always that if you over securitise it, then you end up making trains difficult to use," he told RFI. "And trains are such a fundamental part of movement around the European Union, so they have to be careful not to do that.
Tightening security across the whole network would be "impractical and probably prohibitively expensive", he argues.
Instead he predicts that what we are likely to see emerge is more random police visibility in random places around the train network similar to the scattered presence of air marshals on planes.
"This has a deterrent effect ... something you can do without having to ensure that there is an armed policeman on every train, in every carriage."
EU ministers from the nine countries concerned; France, Germany, United Kingdom, Italy, Spain, Belgium, Luxembourg, the Netherlands and Switzerland also called on the European Commission to reinforce legislation on gun control.