North Korea already cancelled a meeting with the Seoul, protesting joint U.S.-South Korean military drills.
To date, the NR-1 mini-sub is the only nuclear-powered research submarine ever built or operated.
The defection was the first one involving a military officer since 2008 and the 14th involving a soldier since 2000.
The Navy commander's superiors lost confidence in her ability to effectively lead sailors and carry out her duties.
Lt. Col. Marcus Mainz was abruptly relieved in the middle of a deployment in the U.S. 5th Fleet.