In a statement, a spokesman said Krzystof Charamsa would not be able to continue in his senior position in the Vatican and that his future as a priest would be decided by his local bishop.
The Vatican's statement was issued as Charamsa was giving a press conference in Rome, expanding on the reasons for his move he first outlined in interviews with Italy's Corriere della Sera and the Polish edition of Newsweek.
"Msgr Charamsa will certainly be unable to continue to carry out his previous work in (Vatican body) the Congregation for the Doctrine of the Faith and the Pontifical universities, while the other aspects of his situation shall remain the competence of his diocesan Ordinary."
"I know that I will have to give up my ministry which is my whole life," he told Corriere.
The priest said he wanted to challenge what he termed the Church's "paranoia" with regard to sexual minorities, claiming the Catholic clergy was largely made up of intensely homophobic homosexuals.
His action came on the eve of a three-week meeting of bishops which will review Catholic teaching on the family, including the divisive issue of the Church's approach to lesbian and gay believers.
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