Interior ministers from France, Germany and several other countries said checks within the Schengen zone, first introduced tot tackle Europe's migrant crisis, are still needed to deal with terrorist threats.
However, Slovakia said the border checks, first introduced as the migrant crisis peaked in 2015, were not needed for security and warned of undermining Schengen's freedoms.
"The proposed changes in the Schengen borders code will make Schengen stronger and more resilient," European home affairs commissioner Dimitris Avramopoulos told a press conference after talks with the ministers in Luxembourg.
"I reiterated to ministers today the need for a quick compromise on this issue," the Greek commissioner said.
However, a European diplomat told AFP that bridging the divide will take at least a year. Another diplomat said that, besides Slovakia, Slovenia, Hungary and Poland opposed prolonging checks.
The proposed change is "more political than a professional one," Slovak interior minister Robert Kalinak told reporters, adding there was no information that recent attacks were committed by people crossing Schengen borders.
The European Commission, the executive branch of the 28- nation EU, had said several times in the last few months that the extensions must end in November as the migration crisis was easing.
The EU has sharply slowed arrivals of asylum seekers and migrants through closer cooperation with Turkey and Libya, gateways from the Middle East and Africa.
But in recent weeks, France, Germany and other countries notified the commission they would extend the checks for another six months beyond November for security reasons, citing current rules.
The Commission last month released plans to allow Schengen countries to reintroduce border controls for security reasons for up to three years.
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