Freilassing (Germany) (AFP) - Barely four minutes after police put out traffic cones to begin Germany's first border controls over a refugee influx surge, three young Syrians crossing on foot from Austria were stopped.

"Can I see your passports, please?" a federal police officer asked, halting the men in their tracks at Freilassing, a key land crossing for travellers between the Salzburg region and the southern German region of Bavaria.

The trio were told to remain on the side of the road to await the police's decision on their fate.

"We have been walking through Europe for 22 days," said 27-year-old Hatem Ali Ahaj, who suffers from asthma and was struggling to catch his breath.

Taking a puff from his inhaler, he recounted how they had fled their homes in the eastern Syrian city of Raqqa after it was seized by fighters from the Islamic State jihadist group.

The men's trek across Europe started in Greece where they caught a bus before resuming their journey on foot through Serbia, Macedonia and Hungary.

After at last arriving by train in the Austrian town of Salzburg, the German border appeared tantalisingly close and the three had cautiously set their hopes on making it to the city of Stuttgart.

"We thought that Germany was the only country that would treat us like human beings," the asylum seeker said.

Unbeknownst to them, they had arrived in German territory just as Berlin announced it was reintroducing border controls after admitting the country could no longer cope with a record inflow of refugees.

Asylum rules that had been relaxed for Syrians were also now to be enforced again.

Although the policy U-turn was implemented with alarming efficiency by police -- with an impressive mobilisation of a dozen police vehicles to the small town of Freilassing, officers appeared uncertain about how to deal with the migrants.

"Hello, we have three Syrians here, what do we do with them?" radioed an officer, about an hour after Ali Ahaj, as well as his 16-year-old brother Maged and their 28-year-old cousin Achmed Mustafa were told to sit and wait.

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Despite what may be an aborted end to their journey further into Germany, the three Syrians said they were not afraid.

"These are the best police I have encountered so far," said Ali Ahaj, after showing the officers his Syrian passport for the third time.

"The first police told me: 'Welcome to Germany'. Then he smiled," he said.

After about 90 minutes, the wait was over.

Police were to escort the men to the nearest refugee reception centre, where they would finally get some rest.

But for the newly instated border officers, the night was just beginning.

The next person to be stopped at the Freilassing crossing was an Italian driver, who turned out to be carrying eight Syrian passengers in his van.