Struggling Schengen was all-but destroyed in 2016 when countries began blocking their borders to stop illegal immigration.
Under the arrangement European citizens can travel without a visa through the designated zone, covering most of the bloc.
However, as scores of migrants from Syria, Africa and all over the Middle East began making their way through Italy and Greece to inland Europe, borders were sealed.
The introduction of border controls was a divisive issue but member states stood their ground, with Hungary and Austria erecting huge fences to stop entry.
It was widely hoped among EU supporters Schengen will be saved but the EU commission has now confirmed an extension of border controls.
Migrants arriving by the thousand saw fences erected around Schengen zone
Border controls have divided EU leaders as many rejected migrants' entrance
Initially, authorities had announced that they would return to the Schengen area by the end of 2016.
In November, however, the EU Commission renewed the border controls again, but only by three months until February 10, 2017.
Dimitris Avramopolulos, European Commissioner for Internal Affairs, said last November: "We believe these three months will be the end of this period."
The aim is "normally to return to a fully functioning Schengen area".
Months later, it is unclear when Schengen will ever work again.
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Most of the migrants appeared to be men as they came to make a new life in Europe
Tens of thousands of migrants crossed borders in a matter of months
The EU Commission wants to allow Germany among others to extend the border controls till mid-May.
As the "Welt" reports, citing informed circles of the EU Commission, the Commission's management agreed on this internally on Friday.
Reasons for the renewed extension include, among other things, the possible continuation of the journey of irregular migrants who are already in Greece or in other EU countries (so-called secondary migration).
In addition, the administrations of Germany and the other states concerned, Austria, Denmark, Sweden and Norway, are still subject to considerable burdens because of the high number of asylum applications.
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Interior ministers will discuss the issue at their informal meeting in Malta on Thursday and Friday.
However, the necessary approval of EU governments to renew the border controls again was considered certain, reports the Welt.
On Thursday German and Austrian interior ministers announced they wanted to extend border controls – something which must be approved by the EU Commission.