The announcement came after photos began circulating on the internet showing Mr Habineza in intimate poses with several women.
Mr Habineza told Rwanda’s The New Times newspaper that he had resigned for personal reasons.
"But when you see people publishing pictures and all that, it is not good for your image as a minister," he said.
The photos, which Mr Habineza says were taken in 2008, were published on Sunday on an opposition website called Le Prophete.
Most of the 11 photos show the minister dancing or cuddling with one woman in particular in a well-furnished room.
The person who posted them said he was a university student and wanted to show how the government was spending lavishly.
The BBC’s Geoffrey Mutagoma in the capital, Kigali, says the affair has become the talk of the town.
He says it is the first time a minister has tendered his resignation in such circumstances.