AVA- The talks, the first between Putin and the Qatari leader for two years, were focused on "boosting bilateral cooperation in various fields... and on the situation in Syria," the Kremlin said in a statement.
More than 2,500 Syrian rebels and civilians prepared to leave Eastern Ghouta on Monday after the largest exodus yet from the opposition enclave, as talks stalled over the final pocket of resistance.
Russia has been militarily involved in support of the forces of Syrian president Bashar al-Assad's government since 2015.
Last June Saudi Arabia, Bahrain, Egypt and the United Arab Emirates broke off diplomatic ties with Qatar which they accuse of supporting radical Islamists.
To counter its regional isolation, Qatar has sought to deepen trade, military and technological ties with the broader international community.
"We count on our Russian friends, with whom we have a cooperative relationship, knowing that Russia plays a significant role in the problems of the Arab world," the emir said at the start of the talks with Putin.
"Even though we have solid ties and mutual trust, we must go further to reinforce our relations in all areas," he added.
In January, Qatar's ambassador in Moscow, Fahad bin Mohammed Al-Attiyah, told the official TASS news agency that Qatar is finalizing a deal to buy Russian S-400 air defense systems.