The Syrian men were arrested during raids involving 500 officers in the towns of Kassel, Hannover, Essen and Leipzig.
German media reports the suspects were planning a co-ordinated attack on a Christmas market in the country’s north west using weapons and explosives.
The six suspects were identified as Syrian citizens aged between 20 and 28 who arrived in Germany as asylum-seekers between December 2014 and September 2015.
The men, who are allegedly members of ISIS, are accused of having prepared an attack with weapons and explosives on a public target in Germany.
Prosecutors said the investigation was still ongoing but said the men had not finished preparing to carry out their attacks.
Germany remains on high alert almost a year after the deadly Berlin terror attack.
Twelve people were killed and 56 injured when an ISIS fanatic ploughed a lorry through Berlin’s Breitscheidplatz Christmas market last December.
Local authorities across Europe have stepped up security at the hugely-popular Christmas markets and other festive events.
Armed police are on patrol at markets across the UK and organisers have installed concrete bollards and metal barriers to stop vehicles smashing into pedestrianised areas.
Staff have been give security training and visitors to the events can expect more bag searches.
And the US officials issued travel advice at the weekend warning Americans visiting markets and festivals in Britain and mainland Europe to stay extra-vigilant.
A US State Department warning says: “Widely-reported incidents in France, Russia, Sweden, the UK, Spain, and Finland demonstrate that ISIS and their affiliates have the ability to plan and execute terrorist attacks in Europe.
“Last year, mass casualty attacks occurred at a Christmas market in Berlin, Germany in December and a nightclub in Istanbul, Turkey on New Year’s Eve.
“While local governments continue counterterrorism operations, the State Department remains concerned about the potential for future terrorist attacks.
“US citizens should always be alert to the possibility that terrorist sympathisers or self-radicalised extremists may conduct attacks with little or no warning.”