Bavaria's Social Ministry calls the new center, which opened in Nuremberg on Monday, unnecessary. A ministry spokesman said attacks on gay or straight individuals would not be tolerated.
Contradicting gay and lesbian groups across Germany, Emilia Müller of Bavaria's Social Ministry said she didn't think LGBT applicants for asylum faced a major risk of attack by other refugees.
Müller said Germany would expect all refugees - regardless of their religion, national origin or sexual orientation - to get along peacefully, adding that the new facility in Nuremberg - which opened on Monday - was surplus to requirements.
First arrivals expected
The shelter, a large apartment leased by gay and lesbian group "Fliederlich," can host up to eight people. The first tenants are expected to move in within the next few days.
The facility is one of four similar properties across Germany expected to be laid on for homosexual migrants over the next few months.
Berlin plans to open an even larger center in March with 120 beds, while Munich and Frankfurt are also considering similar options.
"Fliederlich" has defended its decision to set up a separate facility for LGBT migrants.
"Some Muslims are offended by the presence of homosexuals or transgender people in refugee shelters," the organization's CEO Michael Glas said, adding that there was a risk of confrontation.
Glas said that his group had been contacted by 20 refugees who said they felt threatened in their current shelters.
"Prejudices don't disappear when one crosses borders," he added, referring to the persecution that many gays and lesbians face in their home countries.
Scores of incidents
While data is limited on the threat faced by homosexual refugees, an LGBT association for the states of Berlin and Brandenburg said it recorded 95 cases between August and December last year.
The incidents included physical violence, sexual attacks and threats.
The new shelter has been welcomed by at least one migrant aid organization.
"Large institutions may be particularly problematic for vulnerable people - including children, pregnant women and certainly homosexuals," said Marei Pelzer, a spokeswoman for "Pro Asyl," which has called for a decentralized approach for accommodating refugees.
There are an estimated 600 gay refugees in the Nuremberg area, with an additional 3,500 awaiting residency in the capital Berlin.
mm/ng (AFP, dpa)