The former strategist was appointed as acting national cyber-adviser in February and was expected to be offered the post full time.
President Barack Obama has said that cyber-security is a high priority for his administration.
In May, the President announced plans for securing American computer networks against cyber attacks.
In recent years, US government and military bodies have reported attempts to infiltrate systems by hackers. He announced the creation of a cyber-security office in the White House, and said he would personally appoint a "cyber-tsar".
Ms Hathaway was widely regarded as the person to fill that post after taking on the role as acting senior director for cyberspace for the National Security and Homeland Security Councils in February.
She completed a review of cyber-security for the Obama administration in April.
At the time, Ms Hathaway said the job ahead was "a marathon, not a sprint."
Her successor has not yet been named by the White House.