The suspects, aged 20 to 28, were detained in dawn raids that saw some 500 police officers swoop on residences in the cities of Kassel, Essen, Hanover and Leipzig.
The men are accused of belonging to “the foreign terrorist group that calls itself the Islamic State”, Christian Hartwig, a spokesman for the Frankfurt prosecutor's office, said in a statement.
“The accused are also suspected of preparing an attack on a public target in Germany using weapons or explosives,” Hartwig said.
The investigators believe the men had not yet finalized their attack plan, he added.
But the local Hessischer Rundfunk radio station, citing sources close to the probe, said the accused “had planned an attack on the Christmas market in Essen”, a city in western Germany.
Such an attack would have revived painful memories of last December's truck rampage in Berlin when a failed Tunisian asylum seeker smashed into a crowded Christmas market, killing 12 people.
Police and prosecutors declined to comment on reports citing Essen's Christmas market as the target, which also appeared in Germany's best-selling Bild newspaper.
The six detained Syrians all arrived in Germany as asylum seekers between December 2014 and September 2015, at the height of Europe's migrant crisis.
Prosecutors gave no further details about the case, saying the inquiry was still ongoing.
German daily Die Welt said it was fellow refugees who tipped off the police about the suspects.
German security forces have been on high alert following a spate of Islamist attacks, of which the Berlin rampage was the deadliest.
Last month, police arrested a 19-year-old Syrian suspected of preparing an Islamist terror attack in the country using “powerful explosives”.
Domestic security services estimate there are some 10,300 radical Islamists in Germany.
About 700 of them are considered dangerous and capable of a violent attack.