The Kremlin said the call had been initiated by Berlin.
Both leaders agreed on the need for further support for the Nord Stream 2 gas-pipeline project across the Baltic seabed that was recently targeted by U.S. sanctions, according to a Kremlin account of their conversation.
Merkel and other German officials have been critical of Washington’s sanctions against the twin-line Nord Stream 2, which was expected to be completed early in 2020 until U.S. President Donald Trump signed the sanctions into law a week ago.
Washington is seeking to halt the pipeline amid fears it will increase the Kremlin’s influence over Europe and weaken the leverage of East European countries.
Putin and Merkel also talked about the current crisis in Libya, where Russia recently said it backed a German peace initiative.
Turkey this week said it was ready to send troops if requested by the internationally recognized government there, which is battling advancing troops loyal to a rival government led by Khalifa Haftar.
Moscow has warned Turkey against such a deployment.
A German government spokesman said Putin and Merkel on December 29 agreed on a further exchange to step up “diplomatic efforts to find a solution” in Libya.
The Kremlin suggested that German and UN mediation could play a significant role in that oil-rich North African country’s fate.
Libya descended into chaos and warfare after the ouster of longtime ruler Muammar Gaddafi in 2011.
The Russian and German leaders also talked about the ongoing war in Syria, where Russian-backed Syrian government troops have kept up furious attacks on the last major rebel stronghold, in Idlib.
There were no details reported from that discussion.
The United Nations has warned of a humanitarian catastrophe as hundreds of thousands of Syrian civilians flee the area, most of them bound for Turkey.
Turkish President Recep Tayyip Erdogan recently warned of the effects on Europe of a new influx of conflict-driven migration from Syria, and sent a delegation to Moscow the next day to clarify the Russian and Turkish positions.
Erdogan suggested Europe will “feel the impact” if the violence doesn’t cease and the refugee numbers ease.
Putin and Merkel also were said to have agreed that the 200-or-so-strong prisoner swap between Ukraine’s government and Russia-backed separatists on December 29 was a welcome development.
Russia insists it is not a party to the eastern Ukraine conflict, despite significant evidence to the contrary.
But its forcible annexation of Crimea from Ukraine in 2014 and its ongoing role in the five-year war in eastern Ukraine have kept U.S. and European sanctions in place and grated on already poor relations between Moscow and the West.