The Mars Atmosphere and Volatile EvolutioN mission, or MAVEN, was set for launch as early as Nov. 18.
"I learned this morning that NASA has analyzed the MAVEN mission relative to the Anti-Deficiency Act and determined that it meets the requirements allowing an emergency exception," Bruce Jakosky, MAVEN's lead scientist based at the University of Colorado in Boulder, said in an email to the Los Angeles Times.
MAVEN will be a crucial communications relay between Earth and the Mars rovers Curiosity and Opportunity, he said, replacing the aging Mars Odyssey, launched in 2001, and the Mars Reconnaissance Orbiter that went into orbit around the Red Planet in 2006.
During the government shutdown NASA has furloughed 97 percent of its nearly 18,000 workers, putting all but the most essential activities on hiatus.
If MAVEN had missed its launch windows it could have been grounded for several years until the alignment of Earth and Mars provided the next available launch window, NASA said.
Scientists welcomed news of the go-ahead for the MAVEN mission.
"Wow, that's good news," UCLA planetary scientist David Paige, who was not involved in the mission, said.
"The whole notion that they wouldn't launch this thing is just appalling," he said. "You have this whole rocket almost on the launchpad."