National Aeronautics and Space Administration officials said Obama accepted Robert Cobb's resignation, effective at the end of this week.
The Project on Government Oversight, a non-profit organization that investigates alleged federal misconduct, said Cobb has been under pressure with Sens. Claire McCaskill, D-Mo.; Jay Rockefeller, D-W.Va.; and Chuck Grassley, R-Iowa, calling for his dismissal.
POGO officials said the senators accused Cobb of maintaining ineffective audit records and called for his removal due to "stalled investigations, whistleblower retaliation and improper social relationships with the NASA officials whose work he was tasked with overseeing."
In his resignation letter, Cobb wrote: "A new Inspector General will find an organization with extraordinarily talented employees dedicated to rooting out fraud, waste, and abuse and promoting the economy, efficiency, and effectiveness of NASA.
"At NASA, the seemingly impossible is turned into marvels of human achievement," Cobb added. "Challenges facing NASA are many, but I am confident that they will be ably met by your administration, working with NASA's gifted scientists, engineers, institutional leaders, and contractor workforce."
Cobb was appointed NASA inspector general in 2002 by President George W. Bush.