The Freedom From Religion Foundation is claiming it won a “major victory,” after the Internal Revenue Service reportedly agreed to adopt standards for determining and investigating whether churches and religious organizations are in violation of restrictions on political activity.

FILE - This March 22, 2013, file photo, shows exterior of the Internal Revenue Service building in Washington. As the United States attempts to punish Russia for its actions in Ukraine, the Treasury Department is deploying an economic weapon that could prove to be more costly than sanctions: the Internal Revenue Service. This summer, the U.S. plans to start using a new anti-tax evasion law that will make it much more expensive for Russian banks to do business in America. (AP Photo/Susan Walsh, File) AP Photo/Susan Walsh, File

AP Photo/Susan Walsh, File

A government letter submitted to the atheist group in the midst of the now-dismissed lawsuit indicates that officials have continued monitoring which churches “merit a high priority examination,” though it is unclear how alleged infractions are being handled.

Dan Barker, co-president of the Freedom From Religion Foundation, told TheBlaze Monday that his organization was assured by the IRS that the agency isn’t offering a special allowance to churches.

“[They assured] our attorney Rich Bolton who’s dealing with them,” Barker explained. “It was conference calls — basically assured … that they now have someone in place who will resume their normal practice.”

After gaining these assurances, the Freedom From Religion Foundation decided to drop the case and to continue monitoring how the IRS proceeds with church infractions, as TheBlaze previously reported.

U.S. District Judge Lynn S. Adelman approved a joint motion for dismissal between the atheist organization and the IRS last week. The court document notes that the Freedom From Religion Foundation is satisfied that the tax authority no longer has “a policy … of non-enforcement specific to churches and religious institutions.”

Adelman dismissed the case without prejudice, which means that the organization has the right to launch another lawsuit in the future if it feels the IRS is not upholding its pledge to hold churches accountable.

In court documents filed last week, the Freedom From Religion Foundation also affirmed that it had received “information” about the IRS upholding policies governing churches. The group’s own motion for dismissal memo includes a June 27 letter indicating that “the IRS has a procedure in place for ‘signature authority’ to initiate church tax investigations/examinations.”

In the letter, which was originally sent to the Department of Justice by Mary Epps, acting director of the IRS’s exempt organizations examinations — the government body that ensures organizations are abiding by tax law — Epps said that 99 churches “merit a high priority examination.”

As of June 23, 2014, records showed that 15 churches allegedly violated tax law in 2010, 18 did so in 2011, 65 did in 2012 and only one was seen as possibly violating the law 2013, though it is unclear how, if at all, these churches are being further investigated or punished.

Image source: Freedom From Religion Foundation/Justice Department

Image source: Freedom From Religion Foundation/Justice Department

All IRS investigations are currently on hold as the agency deals with ongoing scandal for allegedly unfairly targeting conservative groups.

A message left for Bolton, an outside attorney that the Freedom From Religion Foundation hired to tackle the IRS case, was not immediately returned.

“Our victory ensures that churches are not being singled out for preferential treatment as they were — with the IRS turning a blind eye to such events as the annual Pulpit Freedom Sunday,” Freedom From Religion Foundation co-president Annie Laurie Gaylor added in a statement addressing the matter.

At the core of the Freedom From Religion Foundation’s lawsuit is the Johnson Amendment, a controversial IRS code added in 1954 that precludes nonprofit organizations — churches included — from engaging in campaign activity.

The Freedom From Religion Foundation and conservative groups have long clashed over the issue of church politicking, with the conservative legal firm Alliance Defending Freedom organizing the annual “Pulpit Freedom Sunday” event.

The initiative encourages pastors “to reclaim their right to speak freely from the pulpit by preaching an election-related sermon.” The next event will be October 5.