Angela Merkel’s generous open-door policy towards people fleeing Syria’s civil war has been thrown into confusion after Berlin announced that the hundreds of thousands of Syrians entering Germany would not be granted asylum or refugee status. The announcement from the interior ministry on Friday showed panic at the top in Berlin, with the swiftly issued semi-denials only intensifying the sense of confusion and knee-jerk responses over refugees.

Syrians would only be allowed to enter Germany for one year, are barred from having family members join them, and would only enjoy “subsidiary protection” which limits their rights as refugees, the interior ministry announced.

Germany, along with Sweden and Austria, has been the most open of the countries in Europe to take newcomers over the last six months, with the numbers entering Germany dwarfing those arriving anywhere else. However, the interior minister, Thomas de Maizière, announced that Berlin was starting to fall into line with governments elsewhere in the European Union, who were either erecting barriers or acting as transit countries and limiting their own intake of refugees.

“In this situation other countries are only guaranteeing a limited stay,” De Maizière said. “We’ll now do the same with Syrians in the future. We’re telling them ‘you will get protection, but only so-called subsidiary protection that is limited to a period and without any family unification.’”

An interior ministry spokesman told the Frankfurter Allgemeine Zeitung: “The federal office for migration and refugees is instructed henceforth to grant Syrian civil war refugees only subsidiary protection.”

De Maizière described the new regime as “a win for security and order for Germany”.

But the social democrats (SPD), Merkel’s junior coalition partner, promptly disavowed the policy shift and De Maizière later backtracked. “Things remain as they are until there is a decision,” he said. “No change”.

The apparent major policy shift in Berlin followed a crisis meeting of her cabinet and coalition partners on Thursday. In August, Merkel won global plaudits by suspending EU immigration rules to declare any Syrians would gain refugee status in Germany, but also caused consternation among her EU partners who were not forewarned of the open policy.

Thursday’s meeting decided against setting up so-called “transit zones” for the processing of refugees on Germany’s borders with Austria, but agreed on prompt deportation of refused asylum claimants.

Until now Syrians – as well as Iraqis and Eritreans – entering Germany have been virtually guaranteed full refugee status, meaning the right to stay for at least three years, entitlement for family members to join them and generous welfare benefits.

Almost 40,000 Syrians were granted refugee status in Germany in August, according to the Berlin office responsible, with only 53 having to settle for “subsidiary” status. That appears to have ended abruptly.

If confirmed, the suddenness of the move by Germany, which has proven to be pivotal in managing the EU’s biggest ever immigration crisis, will ripple across Europe with unknown consequences. It will particularly test the in transit countries of the Balkans and central Europe through which hundreds of thousands have been trekking to reach Germany in recent months.

New curbs will encourage these countries to establish barriers of their own against the incoming wave of refugees. Merkel is also pressing countries such as Croatia, Slovenia, and Serbia to establish “reception centres” or camps where refugees can be processed and screened before they reach Germany. The countries are resisting because no one knows what to do with those who are screened and do not pass muster for passage to Germany.

Berlin is the most powerful advocate of sharing the refugee burden across the EU, but has also frustrated and angered several of the other countries with a series of unilateral decisions that have had huge knock-on effects across the union.