Novikova worked for NTK television, part of the Alma-Media group, which until recently was co-owned by the president's former son-in-law, Rakhat Aliev.
The ministry said it does not rule out the possibility that Aliev, who reportedly had a personal relationship with Novikova, was involved in her disappearance.
Aliev is wanted in Kazakhstan on charges of abduction, assault, and money laundering. He was arrested by Austrian authorities in June and later released on bail.
(with material from agency reports)