German officials said Merkel is expected to try to persuade Putin to join the European Union and United States in moves to refer Iran to the United Nations Security Council.
Merkel's one-day Moscow visit is also expected to include a meeting with representatives of Russian human rights organizations.
The Human Rights Watch group has urged Merkel to use her visit to emphasize the importance of Russia respecting international human rights standards. The group has accused Merkel's predecessor, Gerhard Schroeder, of ignoring alleged backsliding on democracy in Russia under Putin.
Merkel, who last week met with U.S. President George W. Bush in Washington, took office in November 2005.