The couple married as man and woman in 2015 but the husband underwent a sex change operation and updated his national identity card to read "female", the Straits Times newspaper reported.
But when the unidentified couple tried to buy a government-built apartment, they had to inform the authorities. Married couples receive state grants for first-time purchases of government apartments.
The marriage was voided several months later, making them ineligible to buy the apartment they wanted, the paper said.
Singapore's Registry of Marriage said it would not give details on individual cases but cited the country's laws which state marriage is a union 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," it said in a statement.
Despite calls for change, Prime Minister Lee Hsien Loong has said the country is not yet ready for same-sex marriage since society is still conservative.
Source: AP
Singapore maintains legislation dating back to British colonial rule making sex between men a criminal act although it does not actively enforce the law.
Jean Chong, who co-founded Sayoni, a Singapore-based lesbian advocacy group, told AFP that "policies need to catch up with the realities of society".
"Families come in all shapes and sizes and of course while people get married as man and woman, there are those who transition along the way, so does this mean their marriage is no longer valid?"
Taiwan's top court ruled in favour of gay marriage in May, paving the way for the island to become the first place in Asia to legalise same-sex unions.
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