Mottaki on Thursday delivered a verbal message from Iranian President Mahmoud Ahmadinejad to Qatar's emir Shaikh Hamad bin Khalifa al-Thani, the official Qatar News Agency QNA reported.
It said the message dealt with "relations between the two countries and developments in the region".
Mottaki also discussed ways of boosting Iran-Qatar ties as well as "developments on the regional and international scenes" with Qatari counterpart Shaikh Hamad bin Jassem bin Jabr al-Thani, QNA said.
Mottaki flew into the Qatari capital from the United Arab Emirates, after postponing a trip to Saudi Arabia amid a row between Riyadh and Tehran over alleged Iranian interference in violence-ravaged Iraq.
Saudi Arabia has accused Shia Iran of meddling in Iraq's affairs, a charge denied by Tehran.
Mottaki has also visited Kuwait, Bahrain and Oman on his first tour of Gulf Arab states since he assumed office in August under the hardline Ahmadinejad.
The tour comes to the backdrop of an escalation of Iran's standoff with the West over its nuclear programme.
Mottaki's visit to Qatar coincided with that of the US coordinator for Iraq, James Jeffrey, who also held talks on the situation in Iraq with the Qatari foreign minister, according to QNA.
Jeffrey, a senior adviser to US Secretary of State Condoleezza Rice, met Saudi leaders in the Red Sea city of Jeddah on Tuesday, two days after Arab ministers meeting in Saudi Arabia agreed to send the Arab League chief to Baghdad to organise a reconciliation conference.
In related news, Kuwait's al-Qabas daily has quoted "Gulf diplomatic sources" as saying that efforts are underway behind the scenes to convene a summit conference for Iraq's neighboring countries following the Eid Fitr holiday in Jeddah.
The summit is to discuss the ramifications of the political and security situation in Iraq.
The sources added that the Syrian leadership, in response to a Saudi-Egyptian initiative, expressed readiness to deploy over 40,000 soldiers along the borders with Iraq to strengthen security.