For Women Scotland has claimed in a submission to Holyrood's Justice Committee that it could face prosecution over the position in takes on women's rights in relation to transgender identity.
The issue has sparked angry clashes in recent years between both sides of the debate, particularly over plans to reform the Gender Recognition Act in Scotland.
The Hate Crime Bill has already provoked criticism over potential curbs on freedom of speech and Justice Secretary Humza Yousaf has already indicated that he is ready to change some of the more controversial measures before it becomes law.
For Women Scotland fears that prosecution could hang on "subjective" definitions in the Bill which cover "threatening, abusive, insulting, stir up and likely."
"The provisions on “stirring up hatred” and “possessing inflammatory material” are particularly worrying as it is highly likely that our organisation will be legislated out of existence if this Bill is to become law," it states.
"We are frequently referred to as anti-trans, transphobic, and a hate group who must be silenced ‘by any means necessary’ - which undoubtedly would include reports to the police if the proposed hate crime Bill was law. It would be naive to assume otherwise."
The submission claims that the Bill is "fundamentally flawed" and that women are likely to face charges for public pronouncements they make in relation to the transgender debate.
But a spokesperson for the Scottish Trans Alliance said 71% of all LGBTI people do not report hate crimes that they have experienced.
"It is important that the ultimate determination of what is or is not a crime be done by the police, the prosecutors and the courts,” the spokesperson said.
"In order for them to do this, people need to be encouraged to report all incidents that they feel might elevate to the level of being a crime.
“Scottish Trans Alliance strongly believes in a society where people are free to engage in civil debate, even when the topics being debated are controversial or uncomfortable. There is an obvious difference between civil debate and engaging in or encouraging others to behaviour that is threatening or abusive.”