Lockheed Martin said Friday that incoming chief executive Christopher E. Kubasik has resigned because of a “lengthy, close, personal relationship with a subordinate employee.” (Jeffrey MacMillan/For The Washington Post)

Bethesda-based contracting giant Lockheed Martin said Friday that incoming chief executive Christopher E. Kubasik has resigned because of a “lengthy, close, personal relationship with a subordinate employee.”

Marillyn A. Hewson, who was in line to become president and chief operating officer, will become chief executive of the defense contractor, effective Jan. 1.

The revelation brings Kubasik’s term as chief of the company to a close before it even started. Previously Lockheed’s chief operating officer and president, Kubasik had been preparing for a Jan. 1 handoff of the company’s reins from chief executive Robert J. Stevens.

A Lockheed employee since 1999, he had been groomed for the chief executive job, serving previously as chief financial officer and heading the contractor’s electronic systems business.

In a call with reporters Friday, Stevens, who is also Lockheed’s chairman, said an employee alerted officials in October. Lockheed hired an outside firm to investigate, before asking Kubasik to resign.

“I’m deeply disappointed and genuinely saddened by Chris’s actions,” Stevens said Friday. “We have a code of ethics and business conduct in our company that applies to every person, and having a close personal relationship with a subordinate employee clearly violates that code of conduct.”

The shake-up comes at a difficult time for the world’s largest defense contractor, which has been trying to rapidly reposition itself in response to a slowdown in federal spending. In recent years, Lockheed has laid off employees, bought out top executives and consolidated facilities as it sought to slim down.

The company said the relationship would not affect the company’s operational or financial performance.

Calls to Kubasik’s home were not returned. Stevens, who provided limited details about the relationship, said the employee involved no longer works for Lockheed.

Lockheed’s board of directors had a special meeting Friday, where, Stevens said, he recommended promoting Hewson to the role of chief executive. She has led the contractor’s electronic systems unit since January 2010 and has been with Lockheed for 29 years.

She is now set to take over the chief executive role on Jan. 1. The sudden turn of events means Hewson will become the company’s first female chief executive, and her ascension comes as Phebe N. Novakovic takes over as chief executive and chairman at rival Falls Church-based defense contractor General Dynamics on Jan. 1.

Stevens said Friday that the company will not start 2013 with a chief operating officer but will instead rely on its executive vice presidents, who head the company’s business units.

The contractor said last month that it is splitting its electronics systems business — which Hewson heads — into two new units, missiles and fire control, and mission systems and training, as of Dec. 31. Along with aeronautics, space systems, and information systems and global solutions, it will now have five business units.

Stevens promised Friday to take an active role in the transition process throughout 2013. Although, he said, he had been phasing out his role, he, with Hewson, will “rework that plan to some extent.”

He said Kubasik’s departure should create no lasting problems for Lockheed.

“I don’t believe the company’s in crisis,” he told reporters. “We’ve acted cleanly, clearly and decisively. . . . The very good news is that we have a significant bench strength of executive talent in this company.”