Stalin deported Crimean Tatars to Central Asia en masse during World War Two, accusing them of sympathising with Nazi Germany, and many died in gruelling conditions on arrival in exile.
The Muslim Tatars were allowed to return in the waning days of the Soviet Union, whose 1991 collapse left Crimea in an independent Ukraine. They now make up 12 percent of the Crimea peninsula's mostly ethnic Russian population of 2 million.
Many boycotted the March 16 referendum in Crimea in which an overwhelming majority of voters supported joining Russia, whose annexation of Crimea in April sparked the biggest crisis in relations between Russia and the West since the Cold War.
"I have signed a decree to rehabilitate the Crimean Tatar population, the Armenian population, Germans, Greeks - all those who suffered (in Crimea) during Stalin's repressions," Putin told a State Council meeting shown live on state television.
He was speaking as tension between Russia and Ukraine continued with an agreement last week to avert wider conflict faltering.
Putin's order appeared aimed at easing minorities' concerns about joining Russia by depicting Moscow as a supporter, not an oppressor, and calling for measures to encourage the "national, cultural and spiritual renaissance" of the minority groups.
The decree, published on the Kremlin website, said it aimed "to restore historical justice and remove the consequences of the illegal deportation (of the groups) and the violations of their rights."
It said Russia would "foster the creation and development of national-cultural autonomies" for the groups - implying little change for the Crimean Tatars, who have their own assembly - and allow for basic education in their native languages.
Putin and Turkish Prime Minister Tayyip Erdogan have discussed the Crimean Tatars, who are Sunni Muslims of Turkic origin, at least twice since March. Crimea faces Turkey across the Black Sea.