His comments came less than a month before Russian President Vladimir Putin is to visit Japan for talks aimed at progress on the decades-old territorial row. Moscow has already said it hoped the deployment would not damage efforts to settle the dispute, as reported by Reuters.
Russian media reported on Tuesday that Bastion and Bal anti-ship missile systems were now in operation on the islands, part of an archipelago in the Pacific Ocean over which Russia and Japan have staked rival claims for 70 years.
Read alsoTASS: Putin expects compromise on disputed Kuril Islands will be found one dayThe feud over the islands, called the southern Kuriles in Russia and the Northern Territories in Japan, has kept Tokyo and Moscow from signing a peace treaty to formally end World War Two.
"The four islands are our country's inherent territory. We have conveyed through diplomatic routes that this ... is not compatible with our country's position and is regrettable," Abe told parliament's upper house.
Delicate diplomacy is underway to prepare for the meeting between the Russian and Japanese leaders in Japan on December 15-16. Both sides have said they hoped progress could be made towards settling the dispute.
Abe, who sees improved ties with Moscow as a counter-balance to a rising China, hopes the lure of economic cooperation will help ease a breakthrough when he meets Putin, given the hit to Russia's economy from sluggish oil prices and Western sanctions imposed after its annexation of Crimea.