The unidentified couple were married as man and woman in October 2015, before the husband had sex-change surgery to become a female, according to local daily the Straits Times.
But their marriage was voided by officials in February, after the couple, who were applying for a government-subsidised flat available for married couples, informed authorities of the sex-change, the report added.
Same-sex union is not recognised in Singapore, a city-state famous for its strict social rules.
OutRight Action International, a New York-based group that campaigns for lesbian, gay, bisexual and transgender (LGBT) rights globally, described the move as unprecedented and unacceptable.
“This is a blatant discrimination by two government departments that are undermining the rights to family and housing eligible to heterosexual married couples”
its Asia programme coordinator, Grace Poore, said.
“Singapore’s insistence that transgender people must remain in heterosexual relationships denies transgender people the right to be gay or lesbian, which is completely unacceptable.”
Singapore’s Registry of Marriages refused to confirm details of the case, but said local laws only recognised a marriage between a man and a woman.
“At the point of marriage, a couple must be man and woman, and must want to be and want to remain as man and woman in the marriage,” a spokesperson said in an emailed statement to the Thomson Reuters Foundation.
Transgender people who have undergone sex-changes can legally change their gender on official documents in Singapore.
But campaigners said despite this legal recognition, transgender people still face a wide range of social stigma, from difficulty finding jobs to rejection by their families.
Sex between men, meanwhile, is punishable by up to two years in jail in the island state, although prosecutions are rare.
Taiwan’s top court ruled in favour of same-sex marriage in May, paving the way for the island to become the first place in Asia to legalise gay unions, but progress of LGBT rights elsewhere in the region has been slow (Thomson Reuters Foundation).