It believes the measure could be an effective way to cut smoking among young people who cannot afford to buy larger packs, but can scrape together enough cash for packs of five or ten cigarettes.
The commission is intent on reducing smoking among children and adolescents.
To this effect, it has put forward a raft of proposals to toughen up EU anti-smoking legislation, including:
He said: "It is a well-known fact that if you haven't started smoking in your adolescence you are not likely to pick up the habit at all.
"Therefore we have to counter the efforts of the tobacco industry which aim at recruiting smokers amongst young people to compensate for the middle aged and older customers they lose due to smoking related disease."
The Commission now wants EU health ministers to discuss the new plans at talks in Luxembourg later this month.
Governments are also being urged to oblige tobacco manufacturers to disclose how much they spend on advertising, marketing and sponsorship campaigns.
Passive smoking is also a Commission target with pressure on member states to provide "adequate" protection from exposure to smoking at work.
Advertising
Clive Bates of anti-tobacco group Action on Smoking and Health, said the Commission should concentrate on banning tobacco advertising, and on measures to reduce passive smoking.
He said: "We are very sceptical about tackling smoking by restricting supply to young people.
"Our research shows that British kids show great ingenuity when it comes to sidestepping restrictions, for example older kids will buy a full packet and sell individual cigarettes to younger kids and take a commission and these measures make cigarettes seem like forbidden fruit.
"The only real way to tackle youth smoking is to make it no longer seem like the norm in adult society. That means more smoke-free places, no tobacco advertising and more adults quitting."