Putin put the Northern Fleet on full combat readiness in a snap inspection of Moscow's military power in the strategic region.
"New challenges and threats to our military security demand a further raising of the military capabilities of our armed forces," Defence Minister Sergei Shoigu said.
A military spokesmen said that some 5,000 troops were also being drilled in Russia's far-east and a further 500 close to the volatile southern Caucasus region, news agencies reported.
The drills are the latest in a succession of large-scale military manoeuvres that Moscow has ordered around the vast nation with relations with the West at a post-Cold War low over the crisis in Ukraine.
Ukraine and its Western allies have accused Moscow of pouring thousands of troops over the border to spearhead a pro-Russian uprising aimed at halting Kiev's pivot towards Europe and the United States. Moscow denies the allegations.
The start of the drill came as Putin appeared in public at a meeting with the leader of ex-Soviet Kyrgyzstan after a ten-day absence that had sparked a flurry of rumours about his health.
Moscow has made its frozen Arctic north a key strategic region as global warming spurs international jostling for the spoils of the area's vast natural resources.
Norway is currently conducting some of its largest military exercises in decades not far away from its border with Russia.
That exercise, called "Joint Viking", involves over 5,000 personnel and is presented by Oslo as the largest drill in that part of the country since 1967.