PORTSMOUTH, N.H. – A federal judge has ordered that workers and companies affiliated with Pan Am airline restore to the status quo pay rates and working conditions of pilots and flight crews and refrain from using a nonunion company to conduct business.

U.S. District Judge Joseph DiClerico Jr. issued the order Monday, acting on a recommendation by Magistrate James R. Muirhead. In a Sept. 17 report, Muirhead said that failure to stop Pan Am from continuing to shift work to Boston-Maine Airways, a nonunion company, would cause “grave” harm to remaining Pan Am pilots.

An unidentified lawyer for Pan Am, the only passenger carrier operating out of the Pease International Tradeport, told Muirhead the airline plans to close by Oct. 31 and that Boston-Maine intended to continue its operations. John Nadolny, a lawyer for Pan Am, said Thursday the company would not comment on anything related to the litigation.

The Airline Pilots Association International, which represents the pilots and flight crews at Pease, sued the airline’s parent company earlier this month. They said the company, Guilford Transportation Industries, violated federal labor laws by firing union officers, ignoring the grievance process and trying to shift Pan Am operations to Boston-Maine Airways.

Pan Am, Guilford and Boston-Maine contend that the two airlines are completely separate, but Muirhead disagreed.

“The evidence shows that Pan Am and Boston-Maine operate a joint reservation system that may be accessed from either the Pan Am or Boston-Maine Web sites,” Muirhead wrote. “In addition, a route map on the Boston-Maine Web site shows both Pan Am and Boston-Maine service.”

Muirhead also noted testimony from Linda Toth, who trained Boston-Maine workers and was formerly employed by Pan Am as its southern regional manager. She testified this year that David Fink, the president of Boston-Maine Airways, said “it was going to be smooth sailing with Boston-Maine” after they got rid of “the union jackasses” and that within six months all the planes would be on the Boston-Maine certificate.

Marcus Migliore, attorney for the pilots’ union, said Pan Am, Guilford and Boston-Maine have until Oct. 7 to respond to Muirhead’s report. Ultimately, a federal judge will determine whether to allow Pan Am to go forward with its plans or grant a permanent injunction and implement Muirhead’s recommendations.

Guilford bought Pan Am after the airline went bankrupt in 1998. Once a large international carrier, Pan Am now offers flights from Portsmouth to Orlando and Fort Lauderdale, Fla., San Juan and Aguadilla, Puerto Rico, and Santo Domingo, Dominican Republic.

Boston-Maine Airways offers flights between Portsmouth and Trenton, N.J., Bedford, Mass., and Groton, Conn.

For several years, the union charges, Guilford has laid off Pan Am employees and shut down routes or flights, while expanding Boston-Maine operations to take over routes previously flown by Pan Am.