"There are currently criminal cases launched against 300 individuals," Vladimir Makarov said.
From 800 to 1,700 Russian nationals are estimated to be fighting under the IS banner, according to various reports.
The IS are currently in control of large parts of Syria and Iraq, where the jihadist group declared the establishment of an Islamic caliphate.
IS affiliates also operate in North Africa, Yemen, Pakistan and Afghanistan.
According to the US National Counterterrorism Center, the IS group has attracted at least 20,000 foreign fighters to join the jihadist cause.
Last week Russia froze around 3,500 individual accounts that are suspected of being involved in terrorism and launched 62 criminal cases over financing terrorism.
In early February, Russia submitted a draft resolution to the UN Security Council, aimed at cutting off finance to the Islamic State and Nusrah Front militant groups, operating in Syria and Iraq.