During a 30-minute evening teleconference, Abe requested that Putin implement fully the Ukraine ceasefire deal agreed in February, Japan's foreign affairs ministry said in a statement, AFP reported.
On Monday, EU foreign ministers formally agreed to prolong until January 2016 punitive economic sanctions against Russia aimed at ensuring it fully implements Ukraine peace accords.
The talk between Abe and Putin was held after the Japanese PM pledged at a G7 summit to realize a visit by his Russian counterpart to Japan this year, in order to make progress on territorial disputes over Russian-administered islands off Japan's far north.
Relations between Moscow and Tokyo have been strained for decades over the status of four Pacific islands near Japan's north coast, known as the Southern Kurils in Russia and the Northern Territories in Japan.
Soviet troops seized the islands just after Japan surrendered in World War II and Tokyo says the islands are now illegally occupied by Russia.
The ministry said the two leaders have agreed to continue dialogue and to exchange opinions on Japan-Russia related issues.