Dubbed ETIAS, the proposal is based on a US system that would allow EU countries to quickly cross check identity documents and other details from visa-exempt travellers with a host of data bases.
Nationals from nearly 60 countries currently do not need to have visas to travel the Schengen zone, including those from the United States, Canada, Australia, Japan, Taiwan, Brazil, Chile, Argentina as well as European neighbours like Albania and Bosnia.
The proposal, agreed to on Friday by the interior ministers of EU member countries, still needs to be approved by the European Parliament, but supporters hope to have it in place as early as 2020.
Under the proposed system, citizens from the designated countries would still be allowed visa-free travel, but would have to pay a fee of five euros ($5.60) and submit to the checks.
The fee would also apply to post-Brexit Britain.
"ETIAS will help improve security and protect European citizens," Malta, which currently holds the EU rotating presidency, said in a statement.
The proposal will "allow us to control in advance entries into the EU and better tackle the problems that people who come to commit acts of banditry and terrorism could pose," French interior minister Gerard Collomb told reporters.
The EU is trying to clamp down on security after several European cities were hit by terror attacks claimed by the Islamic State group, while the bloc has also been overwhelmed by the arrival of more than one million migrants.
Under the plan, applicants who wish to travel to the 26-country Schengen zone -- which includes 22 EU countries as well as Norway, Iceland, Switzerland and Liechtenstein -- will electronically pay the five-euro fee for multiple entries over three years.
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