Der Spiegel said the terrorists were members of the Owais al-Qorani Brigade which fought with al-Nusra Front in Syria.
The bogus refugees are wanted for “participation in numerous massacres of captured civilians and Syrian soldiers,” said the magazine, citing intelligence sources.
The Owais al-Qorani Brigade was once an ally of Islamic State but the two groups fell out.
Der Spiegel said one of the wanted men is is a former commander who arrived in the northern German city of Bremen in 2014.
He allegedly took part in a massacre at a rubbish dump where 36 policemen, administrative workers and military officials were beheaded.
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“By God,” the man reportedly said to a friend on WhatsApp in reference to former comrades he met up with in Germany, “they remembered details that I had forgotten myself”.
The individual will appear in court on terrorism offences before the end of the year.
It is unclear whether the group was coalescing in Germany to plan European terror attacks or merely hiding out.
Germany’s domestic intelligence agency (BfV) says hundreds of jihadis arrived among the more than one million migrants who entered the country over the past two years.
The BfV further warned that the growing number of Islamist militants in the country makes further terror attacks “highly likely”.
Germany suffered five Islamist-motivated attacks in 2016, while at least seven other plots failed.
The agency says the number of ultra-conservative Salafists in the country has gone up from 8,350 in 2015 to 10,100 in 2016. Of those, around 680 are classified as “dangerous”.