"I think there are tensions in Schengen there is no doubt about it. And I think it is one of our first tasks to make sure that Schengen remains functioning," Koenders told AFP.
He was speaking shortly after unveiling a new centre in Amsterdam, built on the site of a former military barracks next to the maritime museum, where the EU meetings will be hosted.
"It`s not only about setting the agenda. It`s also about keeping the 28 together," he added.
Last week the EU agreed to rush through reforms to the Schengen zone by the end of the year amid growing concerns about border security in the wake of November 13 Paris attacks that killed 130 people.
The plan would reform the Schengen border code "to allow systematic and obligatory checks at all external borders for all travellers, including those who benefit from free movement," French Interior Minister Bernard Cazeneuve said Friday.
Koenders agreed it was vital that whatever decisions are taken must be respected.
"It`s an historic time in which there`s a lot of lack of confidence in Europe within countries and between countries and sometimes in European institutions," he said.
But he insisted European citizens "don`t want federal dreams". Instead they want a Europe which manages to overcome the problems is facing.
"Of course we are worried about security, because the situation, the risks in the European Union are substantial," Koenders said as the port city prepares to host a flurry of meetings.
But he vowed the necessary measures would be in place to ensure security at the venue in the coming months.
Addressing ambassadors to the Netherlands earlier, he said the Dutch priorities for its EU presidency would focus on the refugee crisis, the European economy, the eurozone and climate change and energy security.
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