Around 400 Kurds had gathered by a Hamburg mosque, which they believed to be used by radicals, to protest against Islamic State insurgent attacks on the Syrian Kurdish town of Kobani. A rival group of 400 hardline Islamist Salafists then formed. Police said they confiscated numerous knives and batons.
Earlier on Tuesday 500 Kurds had protested in central Hamburg, with a group of about 50 briefly blocking rail tracks at Hamburg station.
In the northern German town of Celle, Kurdish demonstrators clashed with an Islamist Chechen group, leaving five people and four police officers injured.
Germany is home to one of Europe's largest Kurdish diasporas. Salafists make up only a tiny proportion of Germany's Muslim population of 4 million but German intelligence says their numbers grew to 5,500 in 2013 from 4,500 the year before.
At least 12 people died in unrest across Turkey on Tuesday, local media said, as the Ankara government's reluctance to intervene militarily in Kobani, which sits on the Syrian-Turkish border, stirred tensions with Turkey's Kurdish minority.
On Wednesday, US-led air strikes pushed Islamic State fighters back to the edges of Kobani, which they had appeared set to seize after a three-week assault. REUTERS