After the closure of the chain, the Chipotle Union filed a complaint with the Labor Board, demanding to organize the main restaurant.

A Chipotle Mexican Grill sign is seen in the Park Slope neighborhood in the Brooklyn borough of New York City.

Michael M. Santiago | Getty Images

A union insisting on organizing workers Chipotle Mexican Grill filed a complaint with the National Labor Relations Board after the burrito chain said it would permanently close the location the union was seeking to form.

In late June, an Augusta, Maine, Chipotle restaurant The union became the chain’s first outlet to file for the election., seeking to be organized under Chipotle United, which is not affiliated with any of the major federations. The petition comes after the employees walked out of the restaurant earlier in the month to protest the working conditions and shortage of staff.

Chipotle said the location has been closed to the public through June 17. Spokesperson Laurie Shallow denied that the restaurant’s permanent closure was due to the union’s plea. Instead, it said the company was unable to provide enough staff for the location.

“Our operations management reviewed this situation as it would any other restaurant with these unique staffing challenges. Chipotle respects the rights of our employees under the National Labor Relations Act,” Shallow said in a statement to CNBC.

But Chipotle United activists, demanding to organize, felt the move was retaliation and held a rally on Tuesday evening to protest the store closures. Organizer Brandi McNeese told CNBC that the closure will only accelerate efforts.

“What they’re doing is fueling us,” McNeese said.

McNeese said Chipotle United, which filed its complaint on Tuesday, primarily concerns crew safety, food security and reduced staffing.

Jeffrey Neil Young, the attorney representing Chipotle United, told CNBC it is “union-busting 101.”

“The closing was targeted not only at Maine workers, but at Chipotle workers across the country who are considering forming a union. Organizing campaigns are underway in Michigan, New York, and elsewhere. Other Chipotle closures have prevented stores from closing. Workers get signals that if they organize, they may be out of a job,” Young said in a written statement. He said the union has asked the NLRB to seek an injunction to force Chipotle to reopen stores and pay back employees until the store reopens.

Employees of a second Chipotle outlet applied for union elections in early July. Employees of that restaurant, which is based in Lansing, Michigan, are seeking to unionize under the International Brotherhood of Teamsters.