Professor Michael Schulz had only just been appointed to the International Theological Commission, a top Vatican body. He teaches Catholic theology at Bonn University.
A spokesman for the Catholic Archdiocese of Cologne said it would inform the state of North Rhine Westphalia, which pays the professor's salary, that Schulz was no longer acceptable because of his changed lifestyle.
The announcement gave no details about his personal relationship, other than to say that Schulz, who was born in 1960, had informed his diocese of origin, the Diocese of Mainz.
He had been suspended from the priesthood after declaring he no longer felt able to practice priestly celibacy.
The Catholic church bars its clergy from taking female or male partners.
Church sources said theology professors who lost church approval usually kept their salaries under the German tenure system, but had to move to other teaching jobs.
The church has the right to nominate all teachers at state-funded Catholic schools.
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