"Oleg Blokhin has indeed tendered his resignation," the federation quoted its president Anatoly Konkov as saying.
Konkov did not name any possible replacements for Blokhin.
Blokhin's move to Dynamo was announced on Tuesday and the coach said he would job share for the two World Cup qualifiers against Moldova and Montenegro next month.
Separately, Blokhin announced the national team squad for the October qualifiers, unchanged from that in their September 11 game against England which ended in a 1-1 draw.
- Oleg Blokhin