Muslim organizations said last week they had lost confidence in Professor Muhammad Kalisch, the theologian who oversaw a teacher-training program at the University of Muenster in northern Germany.
Kalisch upset the Muslim community by writing that there was no historical evidence that the Prophet Mohammed existed.
The state of North-Rhine Westphalia said it would accelerate plans to set up a new chair of Islamic education at the university.
Kalisch would keep his professorship but the newcomer would head the training courses.
Germany is preparing to introduce Islam classes for Muslim children in public schools.
The state higher education ministry in Dusseldorf said the appointments process for the new chair would be completed soon, adding that the new chair had been authorized in 2007 but had not yet been filled.
There would be close consultation with the mosque federations over the appointment, a spokesman said.
The appointment is seen as a face-saving way out of the dispute since German university authorities never sack professors on the grounds of public criticism.
A university spokesman praised the outcome, saying Kalisch's field was Islamic theology, not teacher training, and he had not been intended to run the program for teachers.
An estimated 3.3 million people of Muslim background live in Germany, 1.8 million of them Turks.
Source: Expatica (English)