"All political parties should distance themselves clearly from these protests", Maas told Spiegel.
"We can't be silent if a xenophobic atmosphere is being built on the backs on people who have already lost everything and come to us looking for help," he added, referring to the fact that Germany's welcoming of large numbers of refugees has sparked many recent demonstrations.
"We have to be clear: these demonstrators are not in the majority."
Police said that 10,000 people took part in the "Patriotic Europeans against the Islamisation of the West" (Pegida) demonstration, while 9,000 took part in a counter-demonstration.
Appearances on the streets by the group are becoming a weekly occurence, with 7,000 marching last time.
"The initiators [of the Pegida march] are fanning up prejudice and fear with xenophobic and islamophobic agitation," North Rhine-Westphalia interior minister Ralf Jäger told the Neue Osnabrücker Zeitung.
Jäger's own state saw a Pegida demonstration in Düsseldorf which only drew around 400 attendees compared with 1,100 counter-demonstrators.
He and his fellow state interior ministers will discuss an investigation into the organization and motives behind Pegida and other anti-Islam movements at their conference this week.
They are anxious to avoid a repeat of the scenes in Cologne in October, when thousands of 'Hooligans Against Salafists' (HoGeSa) clashed with police in an hours-long street battle.
"You shouldn't allow yourself to be instrumentalized for extremist political aims which you don't yourself share," CDU security policy expert and MP Wolfgang Bosbach told the newspaper.
Organizers of the counter-demonstration in Dresden included members of Christian churches, the Islamic centre, the Jewish community, the Foreign Residents' Association, students and a group called "Nazi-free Dresden".
Around 1,200 police from Saxony and surrounding states were deployed in the city.
Violence was limited to a few fireworks being thrown and scuffles after the demonstrations ended close to the town hall.