WASHINGTON, DC - NOVEMBER 30: United States Supreme Court Justices pose for their official portrait at the in the East Conference Room at the Supreme Court.
CNN  — 

The Supreme Court declined on Monday to step into a religious liberty dispute concerning whether taxpayer funds can be used for historic preservation at churches.

The court decision to stay out of the dispute is a loss for the churches and leaves in place a decision by the New Jersey Supreme Court that held the denial of state funds to religious establishments did not violate the church’s free exercise rights.

However, Justice Brett Kavanaugh, joined by Justices Samuel Alito and Neil Gorsuch, wrote separately to say that while he agreed that the court should not take up this particular case because some of the facts were in dispute, he was troubled by a lower court opinion that went against the churches.

“At some point, this court will need to decide whether governments that distribute historic preservation funds may deny funds to religious organizations simply because the organizations are religious,” Kavanaugh wrote.

Kavanaugh made clear that if another such case made it to the court, he believes that “barring religious organizations because they are religious from a general historic preservation grants program is pure discrimination against religion.”

The case was a follow onto a 2017 Supreme Court opinion that went in favor of a church pre-school that sought state funds – available to nonreligious schools – for playground improvement. The court held the church could not be excluded from a state’s playground resurfacing program solely because of its religious character.

That case left for another day circumstances where state funds would have a closer nexus to the maintenance or repairs of a house of worship. Supporters of the churches hoped the Supreme Court would step in to resolve that lingering question.

This story has been updated.