Several defense companies have stepped back from extensive furloughs of their own workforce following the Pentagon’s decision to recall civilian employees, but warned on Monday that a prolonged government shutdown could force them to proceed with the plans.

Defense giant Lockheed Martin [LMT] said it will furlough fewer employees than originally envisioned, but said others will still be told to stay home because of government-issued stop work orders on programs and limited access to government facilities. Rival Boeing [BA] said the return of the Pentagon’s workforce will delay possible furloughs–for now.

“While the return of these DoD employees has at least delayed the need for furloughs at some Boeing facilities, the continued impact of the government shutdown could still result in furloughs for some employees,” said Meghan McCormick, a company spokeswoman.

Photo by U.S. Navy.

Lockheed Martin said Friday that it would furlough 3,000 employees beginning Monday, but reduced that number to 2,400 after Defense Secretary Chuck Hagel announced the recall of most of the 350,000 Pentagon civilians. Uniformed military personnel were exempted from the furlough that went into effect when the government shut down Oct. 1.

Lockheed Martin said 2,100 of those employees work on government civilian agency programs while 300 of them work on defense. Hagel’s order returned employees to the Defense Contract Management Agency, allowing many of the stalling programs to resume work.

But Department of Homeland Security and NASA are still largely being affected by the shutdown and subsequent furloughs.

Sikorsky, a helicopter building unit for United Technologies [UTX], said Monday it was abandoning plans to keep 2,000 employees home.

Hagel said he was returning most of the Pentagon civilian workforce, including the acquisition community, after Congress passed the Pay Our Military Act (POMA), which would allow almost all Defense Department civilians to work throughout the duration of the shutdown and receive their paychecks on time.

DoD Comptroller Robert Hale said on Saturday that the department had consulted with the Justice Department and concluded that “that the law does not permit a blanket recall of all DoD civilians” but that most could return to work this week.

Some civilians had been excepted from being furloughed from the start, primarily those who support base protection efforts or directly support military operations, Hale said. And some civilians will continued to be furloughed for the duration of the government shutdown, including those in public and legislative affairs, those supporting the Chief Information Officer or the Deputy Chief Management Officer, and others who support actions deemed not covered by POMA.

But for about 350,000 employees globally, the recall will allow personnel to return to work and get paid. These workers include those who support services for military members–health care, family programs, commissaries and other base services–as well as activities that would see down-the-road effects if the workforce were furloughed for too long, such as acquisition, contract logistics, financial management and more.

Hale could not provide exact figures yet, but he said a percentage of furloughed employees somewhere “in the 90s” would likely be recalled.

Hale said the furloughs had “stopped essentially everything except financial management and planning activities in connection with excepted activities like Afghanistan and military operations,” including budget planning for the current fiscal year–which still has not been agreed upon–and planning for the next several years to come.

Though those activities will be able to resume as personnel return, Hale cautioned that there still is no money to purchase anything not directly related to warfighting, “so as our people come back to work, they’ll need to be careful that they do not order supplies and material for non-excepted activities.”

The Air Force curtailed several activities last week as a result of the shutdown, and Air Combat Command (ACC) spokesman Master Sgt. Randy Redman said Oct. 7 that all restrictions remain in place this week despite civilian personnel returning to work.

“Our current activities include those related to named or otherwise directed operations we’ve been ordered to support,” Redman said. “Basically, if units are deploying from now through January, they’re currently flying at the level needed to achieve and sustain full combat readiness in preparation for those deployments.”

But for units not preparing to deploy, operations have been stopped and units stood down.

About 7,500 of ACC’s 10,000 civilians were furloughed. Across the entire Air Force, 104,000 were furloughed, with the majority being brought back this week, Air Force spokeswoman Capt. Erika Yepsen said.

DoD agencies may have fared better than the services during the furloughs. The Missile Defense Agency, for example, did not have to furlough any of its employees last week.

“As a Research, Development, Test and Evaluation (RDT&E) agency within the Department of Defense, the Missile Defense Agency utilizes multiple-year RDT&E funds for personnel salaries,” spokesman Rick Lehner said. “With the beginning of the new fiscal year on Oct. 1, MDA has sufficient FY2013 RDT&E funds available for a limited time to support our personnel payroll.”

He added that he did not believe any major tests or contract awards were being hampered by the shutdown. 

The Navy said all but about 1,000 of the 72,000 employees furloughed were returning to work.