The Islamic extremists "are trying to approach the young unaccompanied refugees, who arrive in our country without their families and are particularly looking for contacts and support," a spokesman for the intelligence service in the southern state of Bavaria told DPA.
He said many of the youths are approached around reception centres but also at Munich railway station where many of the asylum seekers have arrived from Hungary and Austria in recent days.
The Islamic extremists "want to take advantage of the insecurity and distress of the refugees," he said.
On Tuesday, the intelligence services in North Rhine-Westphalia reported similar contacts in their region, noting that Islamic radicals were approaching asylum seekers through fake charities.
"We are going to inform the employees of the reception centres and make them aware of this situation and the methods used for these attempts to approach" the young refugees, said a spokesman in the state, also quoted by DPA.
Under the quota system in Germany, North Rhine-Westphalia and Bavaria are the two regions that receive the most asylum seekers, with 21 percent and 15 percent respectively.
Germany expects to receive 800,000 asylum seekers this year, four times more than last year.
Syrians, who are fleeing their war-torn country, form the largest group.