Controversy over using Russian rocket engines to launch Pentagon satellites has spilled over to potentially threaten the financial viability of certain U.S. civil space programs, according to some aerospace-industry officials.

Escalating congressional battles to restrict RD-180 engines for the military’s workhorse Atlas V rockets already have shaken United Launch Alliance, the Boeing Co. and Lockheed Martin Corp. joint venture that is the Pentagon’s primary launch provider. Now, these officials said, fallout could undermine...