Putin's spokesman Dmitry Peskov said Oleg Morozov, 61, was leaving his post as head of the president's domestic policy department because of family reasons.
Peskov also announced the departure of head of the international cooperation department, Sergei Bolkhovitin, but gave no reason for his removal. His department deals with technical aspects of foreign cooperation.
Morozov was replaced by Tatyana Voronova, who previously headed the youth section of Putin's ruling United Russia party, served as a lawmaker and sat on the country's central elections committee before moving to the Kremlin in early 2013.
Analysts said Voronova is a protege of Vyacheslav Volodin—Putin's first deputy chief of staff who was blacklisted by the European Union last year for what the bloc said was his role in the annexation of Crimea from Ukraine.
Commentators saw her appointment as a possible signal that the Kremlin was gearing up for local elections due in some regions later this year as well as national parliamentary polls due in 2016.
No successor was named for Bolkhovitin.
The sense of intrigue at the Kremlin this month was heightened when Putin vanished from public view for 10 days. The president laughed off his disappearance when he finally re-emerged at a public event on March 16.
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