Alliance Defending Freedom (ADF) has filed legal action against the law which has been newly brought into the state saying that the legislation "punishes" the right to freedom of religious speech of churches.
The law applies to public places including schools and hospitals and says that people should be able to use the bathroom of whatever gender they identify with.
The charity says it is preparing the action on behalf of four places of worship in the state asking that they might be able to run their churches in a way "that doesn't violate their core religious beliefs."
At the start of October the law came into effect in the state to bar discrimination against transgender people using public bathrooms.
On their website it says: "Churches are not businesses. They are private houses of worship.
"The public is welcome to attend church services and events as a guest, but must be respectful of the beliefs and policies of that church.
"Likewise, the state of Massachusetts must respect both a church's First Amendment right to establish polices that reflect and reinforce its faith, as well as its duty to protect the privacy of those who walk through their doors."
ADF stressed that these churches are not discriminating but "simply defending their Constitutional right to operate according to their beliefs - the very beliefs that make the church what it is."
Attorney General Maura Healey would be the person fighting the lawsuit on behalf of the state.
The Catholic Herald reported her spokesperson will review the lawsuit.
"This law is about civil rights and is critical for people who were without full protection and equality under the law for too long," they said.
