"Discussing various aspects of the situation in Ukraine... Putin stressed the importance of holding constitutional reforms" in Ukraine, the Kremlin said in a statement.
Russia has called for Western powers to urge Ukraine to change its constitution to allow greater autonomy for regions in the south and east where ethnic Russians and Russian-speakers are concentrated.
The Kremlin said that Merkel and Putin also discussed Moldova's largely Russian-speaking breakaway region of Transdniestr, which lies on part of Moldova's border with Ukraine.
Putin raised "the need to take effective measures aimed at lifting an effective blockade from the outside of this region," it said.
More From This Section
Russian Foreign Minister Sergei Lavrov said Saturday that "Chisinau and the new Ukrainian authorities have practically organised a blockade" of Transdniestr.
"What's more, the European Union and, as I understand it, the United States, encourage such a line," Lavrov added.
The takeover of Crimea from Ukraine by Russia has raised fears in other ex-Soviet countries of similar moves on Russian-speaking separatist regions.
Officials in Transdniestr this month appealed to lawmakers in Moscow to pass legislation that could see the region absorbed into Russia.
US Assistant Secretary of State Victoria Nuland on a visit to Chisinau on Sunday said the US was giving Moldova an extra USD 10 million to strengthen its borders.
Residents in the region, which has never been recognised as an independent state by any United Nations member, voted overwhelmingly to join Russia in a 2006 referendum and Moscow still maintains thousands of troops there.