Putin warned Merkel in Monday's call that the risk of Ukraine's "unsanctioned draw-off" of the Russian gas supplied to European consumers via a transit pipeline could increase during what is forecast to be a cold winter. The Kremlin said the EU and Russia will continue discussions.
There was no immediate comment from Ukraine.
Past gas disputes between Russia and Ukraine have led to cutoffs. One standoff in 2009 caused serious disruptions in winter supplies to EU countries.
Russia's annexation of Ukraine's Crimean Peninsula and its support for separatist rebels in eastern Ukraine brought relations between the two ex-Soviet neighbors to the verge of full rupture.