Singh expressed the hope that all sides would exercise restraint and work together "constructively to find political and diplomatic solutions that protect the legitimate interests of all countries in the region and ensured long-term peace and stability in Europe and beyond."
Putin, who is facing the prospect of international isolation in the wake of its action, telephoned the Prime Minister at 7.30 pm and discussed the evolving situation in Ukraine and the recent referendum in Crimea.
Thanking Putin for explaining the Russian position with regard to recent developments in Ukraine, Singh "emphasized the consistent position India had on the issues of unity and territorial integrity of countries", an MEA statement said.
Putin, earlier in the day, took the first step to absorb the Ukrainian region of Crimea into Russia, in what would mark the most significant redrawing of Europe's borders since World War II.
Putin officially informed the Russian Parliament of Crimea's request to join Russia and instructed the national branches of power to approve an agreement for Crimea to become a part of the country.
Singh and Putin also discussed the close relationship and mutually-beneficial partnership between the two countries, the statement said.
They reaffirmed the importance that both countries attach to their special and privileged strategic partnership.
The Prime Minister also thanked Putin for his personal leadership in further deepening and strengthening the India-Russia strategic partnership in recent years, it added.