"We're in a crisis situation, with geopolitical earthquakes, notably in the countries of the south. The natural tendency is going to be to protect oneself," Jean Leonetti, France's European affairs minister, told reporters.
"This situation is not illegitimate, but if we don't put in place any safeguard, any system, then we'll end up with moves that differ from one country to another," he said on the sidelines of a European Union meeting in Poland, which is currently at the helm of the 27-nation bloc.
"It would be better to sort out an agreed procedure which can be implemented and would apply to all of use," he added.
Denmark deployed 50 new customs officers at its borders with fellow EU members Germany and Sweden on July 5th, a controversial measure hammered out under pressure from a far-right party which drew criticism from Brussels and its neighbours.
The Scandinavian country argues random checks are in line with Schengen and that their aim is to combat the smuggling of illegal goods and drugs, not to control travellers.
But on Monday the European Commission -- the EU's executive arm -- warned that Copenhagen had failed to justify the move.
At the end of June, EU nations tasked Brussels with setting down criteria under which Schengen members could resume border checks in the event of a spike in migration such as that seen in France, Italy and Malta since the Arab Spring.
The European Commission is to deliver its findings in September.
"In this time of tension, all EU members need systems which match the problems," said Leonetti.
"If we achieve that, we'll at least have fewer proposals from single member states."
"We don't want to stigmatise Denmark. There's no question of elbowing Denmark out of Schengen, neither legally nor politically," he added.