Many organic groups that once praised USDA deputy administrator Miles McEvoy are now fighting his policies in federal court.

When Miles McEvoy was put in charge of the USDA’s National Organic Program in 2009, the appointment was strongly applauded by organic and environmental groups.

Six years later, some of those same organizations are facing off against McEvoy in federal court over his administration of the program.

While the criticisms of his policies are numerous, most boil down to the allegation that McEvoy has weakened independent oversight of the program to make life easier for large agribusiness firms.

“There is a decisive split in the organic community and McEvoy is right in the middle of it,” said Mark Kastel, co-founder of the Cornucopia Institute, an organic watchdog group, who once praised the deputy administrator as “a true believer, not a PR figurehead.”

Prior to joining USDA, McEvoy was instrumental in shaping the organic inspection program at the Washington State Department of Agriculture and was involved in launching other organic programs and organizations.

“I don’t know if we had higher expectations than McEvoy deserved or if he changed,” Kastel says now.

A spokesperson for USDA said the agency “values and has faith in Deputy Administrator Miles McEvoy’s leadership of the National Organic Program.”

The program thoroughly investigates any complaints about non-compliance with organic protocols and it’s inaccurate that USDA’s internal auditors are investigating McEvoy or his department, as claimed by the Cornucopia Institute, the spokesperson said.

A major point of contention is McEvoy’s decision to change the decision-making process for which synthetic substances are allowed to remain in organic production.

Traditionally, synthetic substances were removed from the list of approved organic materials unless two-thirds of the members of the National Organic Standards Board voted to retain them.

In 2013, the USDA changed the procedure so that two-thirds of the board must vote to remove a substance. In effect, a nine-person majority of the 15-member board can vote to remove a substance and its use would still be allowed.

Earlier this year, a lawsuit was filed against McEvoy and his superiors at USDA for allegedly violating administrative law by implementing the new rule without public comment.