Putin opened the meeting with Moldovan President Vladimir Voronin by mentioning efforts to improve relations that have worsened in recent years.
"We also have other problems to discuss, including political issues related to the Trans-Dniester settlement," Putin said at the start of his talks with Voronin which took place in the Russian president's residence outside Moscow.
Trans-Dniester, a province in eastern Moldova mainly populated by Russians and Ukrainians, broke away in 1992 after a bloody war with Moldova which left over 1,500 people dead. Russia helped mediate the conflict and deployed its peacekeepers to monitor a truce.
Russia maintains about 1,500 troops in Trans-Dniester despite calls by the United States and the European Union to respect a 1999 pledge to withdraw them. Russian officials say Trans-Dniester is strategically important for Russia and withdrawing the troops would cause instability.
Repeated efforts to settle the separatist conflict have failed. In 2003, a peace plan drawn up by Putin's aide, Dmitry Kozak, was rejected by Voronin, who warned it could lead to the disputed region becoming a state.
Voronin, a Communist, then moved to bring the impoverished ex-Soviet nation closer to the West and out of Russia's orbit. The Russian-Moldovan relations deteriorated sharply, and Russia imposed a ban on Moldovan wine - its main export - citing sanitary reasons.
Putin on Friday said that his government had drawn proposals to end the ban. Voronin also sounded positive, saying that "practically all obstacles that existed a year or two ago had been removed."
Some analysts speculated that Russia and Moldova had been involved in talks to revive the Kozak plan that would have given complete autonomy to Trans-Dniester while renaming it Moldovan Dniester Republic.
There was no immediate indication, however, of any immediate breakthrough.