The ballot initiative had required at least 60 percent of votes cast in order to pass, a high hurdle to clear in the conservative southeastern state.
The defeat, which was reported by US media, marks the first pro-abortion rights ballot measure to fail since the US Supreme Court in 2022 overturned Roe v Wade, the ruling that had given women a federal right to the procedure.
News network NBC reported that the measure, known as Amendment 4, received 57 percent of the vote, failing by three percentage points.
Anti-abortion activists welcomed the vote result as a major triumph.
"Today's victory in Florida is unprecedented -- and should be viewed as the start of a revolution for women's healthcare in America," Christina Francis of the American Association of Pro-life OB/GYNs said in a statement.
Advocates had hoped Florida, which is surrounded by states with stringent restrictions, could have once again become a destination for those seeking the procedure in the US southeast.
Abortion rights proponents argue that many women still do not know they are pregnant at six weeks. The extension until fetal viability would have allowed the procedure until approximately 24 weeks.
"As the majority of Florida voters made clear tonight, they want their reproductive freedom back," Nancy Northup, president of the Center for Reproductive Rights, said in a statement.
"Due to the high 60 percent threshold and the state's disinformation campaign, they must continue to live with the fear, uncertainty, and denial of care caused by the reversal of Roe," she added.
Florida was one of ten states with abortion referendums on the ballot Tuesday, almost all of which were aimed at safeguarding the right to the procedure or reversing restrictions adopted since the Supreme Court's decision.
