"The chancellor asserted the German position forcefully that the so-called March 16 referendum on Crimea is illegal. It is against the Ukrainian constitution and international law," her spokesman Steffen Seibert said, recounting a phone call between the two leaders.
In a strongly-worded message, Merkel also said that she "deplored the lack of progress that has been made in forming an international contact group to help find a political path and a solution to resolve the conflict in Ukraine".
Seibert added that the German Chancellor had stressed the urgent need to find a result in this area.
Merkel also discussed the Ukraine situation during a telephone conversation with Chinese President Xi Jinping.
According to Seibert, Xi said he was favourable to finding a political solution "through dialogue".
"He emphasised that an end to the crisis should be based on international law," he said.
A statement released by Moscow after Merkels conversation with Putin -- and a subsequent conversation the Russian leader had with the British Prime Minister David Cameron -- asserted the Kremlins position that the pro-Russian forces in Crimea were "legitimate".
Putin wished in particular to stress that "the lawful leadership in Crimea is taking actions based on international law and with the aim of guaranteeing the legitimate interests of the population of the peninsula," Moscow said.
A referendum will be held in Crimea on March 16 to see if the southern Ukrainian region wants to immediately become part of the Russian Federation.