Putin said the plan should not be seen as sabre rattling, but it comes as Moscow is serving as a key ally and arms supplier to Syrian President Bashar Assad during that nation's civil war.
The only naval base that Russia has in the Mediterranean and anywhere outside the former Soviet Union is located in Syria.
Russian ships have been making regular visits to the Mediterranean, but the statements by Putin and other officials mark an attempt to revive a Soviet-era practice, when Moscow had a permanent navy presence in the waterway.
The chief of the military General Staff, General Valery Gerasimov, said on Thursday that Russia currently has 16 navy ships in the Mediterranean.
The defence ministry said it would regularly rotate them to keep a presence of about a dozen.
Speaking at a meeting with the top military brass, Putin said the sea is a "strategically important region, where we have interests connected with ensuring Russia's national security”.
The statement is part of Putins's efforts to boost his nation's military and showcase its power worldwide.
Military officials have said in the past that Russian navy ships in the Mediterranean could be used to evacuate equipment and personnel from the Syrian port of Tartus.
Previous deployments have invariably included amphibious landing vessels, which could serve the purpose.
Analysts and retired naval officers point out that Russia lost much of its navy capability during the post-Soviet economic decline, when the military had to mothball relatively modern ships for lack of funds to maintain them.
The military has commissioned new navy ships as part of a costly military build-up, but their construction has dragged on slowly.
Experts say the current plan will stretch the Russian fleet capability and note that the base in Tartus, a rundown facility made up of a floating pier and a few aging barracks and warehouses, can't provide a sufficient backup for the permanent navy presence in the region.
It's also too small for big ships, which must stay at sea.