Austria, Germany, Denmark, Sweden and non-EU Norway are all allowed to continue the checks which they first introduced in 2015 as a wave of refugees and migrants streamed across Europe.
"Our ultimate objective is to get back to Schengen as soon as possible," said Slovak Interior Minister Robert Kalinak, whose country holds the rotating presidency of the European Union.
"Although we are not there yet, the situation is improving. The prolongation will therefore be for three months only, and there will be more intensive reporting obligations compared to the previous period."