It will also create a bank of disaster information for use by schools caught in a violent attack.
The measures have been drawn up for the European Commission by nuclear scientist Dr Jean-Pierre Massue and are expected to be approved next month.
The measures will be included in an extension of the EU's Daphne project, aimed at improving the safety of women and children across Europe.
"The need for training to increase security in schools is underlined by what happened in Beslan," said Dr Masse.
"It is very important to increase children's awareness, including how to behave in emergency situations."
This is particularly true, he said, as schools are no longer isolated from tensions in society.
Dr Massue belongs to the European scientists' federation, FER, which has already helped to set up an EU network to share information on the psychological effects that catastrophic events have on children.
The EU's Daphne 2 project, to run from 2004 to 2008 with a budget of l50 million (pound;33m), will fund organisations that combat violence against children. In particular it will share information on tackling violence in schools, including terrorism.
The document, now before the commission in Brussels, suggests creating a network of "cities of risk" to share advice on how to prepare schools against terrorist attacks. It would include areas of conflict and possible targets such as London and other capital cities.
Schools would be urged to carry out emergency drills and send selected pupils and teachers for training - dealing with armed assailants, for example. The project would also help schools to set up a security plan which might also include how to cope in siege and hostage situations.
Last year, under the aegis of the Council of Europe, Dr Massue helped to draw up an agreement on risk prevention in schools that would serve as a model for the EU's training programme.