Russia is currently using its older S-300 systems on the peninsula it annexed from Ukraine in March 2014 in a move condemned by the West that led to the imposition of US and EU sanctions.
"In August 2016 the (S-400) systems are expected to be unloaded in Feodosia where they will be permanently located," Yevgeny Oleinikov, deputy commander of the Russian army's 18th surface-to-air missile regiment, told RIA Novosti state news agency, referring to an eastern Crimean town.
The system can track some 300 targets and shoot down around three dozen simultaneously over a range of several hundred kilometres.
Since Crimea's annexation Russia has stepped up its military presence in the peninsula, which is home to its Black Sea fleet.
The move comes as NATO is rolling out the biggest military build-up in eastern Europe since the end of the Cold War in response to a resurgent Russia and the United States has angered Moscow by installing a missile defence shield close to its borders.