EU Migration Commissioner Dimitris Avramopoulos called the meeting after Denmark this week slapped spot checks on its border with Germany, and Sweden imposed its own controls on travellers from Denmark.
"We agreed to keep (the measures) to a minimum and return to normal as soon as possible. This means the flows have to be slowed down," Avramopoulos said following the talks in Brussels with officials from Sweden, Denmark and Germany.
"We all agreed that Schengen and free movement must be safeguarded," Avramopoulos added.
More than a million refugees and migrants arrived in Europe in 2015 -- many of them fleeing the war in Syria -- in the worst crisis of its kind to face the continent since World War Two.
The EU's cherished passport-free Schengen area has come under huge strain, as many countries have reintroduced border controls to deal with the flow of migrants trying to reach wealthy Germany, Sweden and other countries from the main landing point in Greece.
Schengen rules mean checks can be reintroduced for up to six months.
But Swedish migration minister Morgan Johansson said on Wednesday that the new controls "should not be put in place longer than we need".
He said the checks were necessary because his country has taken in more asylum seekers per capita than any other EU nation -- 160,000 asylum requests last year, including 26,000 unaccompanied minors, with 115,000 of them in the last four months.
Danish immigration minister Inger Støjberg said they were "monitoring the situation by the hour" but added that "in Denmark we don't wish to be the final destination for thousands and thousands of asylum seekers."
Støjberg told reporters after the meeting, however, that she informed Avramopoulos that Denmark could implement further measures at its border “if necessary” and with short warning.
German interior ministry official Ole Schroeder said part of the problem was that an EU scheme to relocate 160,000 refugees from frontline Greece and Italy to other member states was not working.