Justice Minister Bekir Bozdag announced the "protecting convicts" measure for homosexual prisoners in a written response to a parliamentary question from an opposition lawmaker.
Turkey's political landscape has in recent months become increasingly polarised between the opposition and Prime Minister Tayyip Erdogan's Islamist-rooted AK Party government, seen as pushing a more conservative agenda on a range of issues.
"Projects are under way for the construction of separate penitentiaries to house inmates with divergent sexual orientations," Bozdag said.
The issue sparked widespread debate this week after the lawmaker who tabled the question expressed concerns.
Some took to social media to criticise it, but a survey of 10,000 people carried out by mainstream daily Hurriyet found that 52% of respondents backed the proposal.