The decision came after Moscow's seizure of three Ukrainian navy ships and their crews.
Russia has steadily poured new military hardware into Crimea since it annexed it from Ukraine in 2014. Moscow's announcement about new missiles comes as it and Kiev try to pin the blame on each other for the confrontation on Sunday.
A Reuters correspondent in Crimea on Wednesday also observed a Russian navy minesweeper ship, the Vice-Admiral Zakharin, heading for the Sea of Azov, which is used by both Ukraine and Russia and is an area of growing tensions, from the Black Sea.
Ukraine introduced martial law in parts of the country after the seizure of its ships saying it feared a possible Russian invasion.
Russian news agencies cited Vadim Astafyev, a spokesman for Russia's southern military district, as saying that a new battalion of S-400 missiles would be delivered to Crimea soon and become operational by the end of the year.
The deployment is likely to have been long-planned, but the timing of the announcement appeared designed to send a message to Ukraine and the West that Russia is serious about defending what it regards as its own territory and waters.
Crimea already hosts three battalions of the anti-aircraft missile systems which have a range of up to 400 km (248.55 miles) allowing Russia to control large swaths of the skies above the Black Sea.
The new deployment will allow it to increase its air defense coverage area.
A Crimean court was due to order the detention of nine of the 24 captured Ukrainian sailors - including senior Ukrainian naval officers and at least one member of Ukraine's SBU intelligence agency - later on Wednesday.
A court in Simferopol, the capital of Crimea, on Tuesday ordered the other 15 Ukrainian sailors to be detained for two months pending a possible trial.
All of the sailors face jail terms of up to six years if found guilty of what Moscow says was a plot to illegally cross the Russian border by trying to pass through the Russian-controlled Kerch Strait on Sunday without advance notice and ignoring calls to stop.
Ukraine says its ships did nothing wrong and have every right to use the strait, the only gateway to the Sea of Azov from the Black Sea, without Russian permission.