The talks got underway at Erdogan's presidential palace in the capital Ankara, the Turkish presidency said.
Erdogan has been a major supporter of Doha in the crisis that has seen Qatar left diplomatically and economically isolated.
On June 5, Saudi Arabia, Bahrain, the United Arab Emirates and Egypt cut ties with Qatar accusing it of backing extremism and fostering ties with their Shiite rival Iran.
Erdogan has strongly spoken out against the sanctions applied by Saudi Arabia, Bahrain, the United Arab Emirates and Egypt against Doha.
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In a show of solidarity, Turkey has also sent cargo ships and hundreds of planes loaded with food products to break the embargo on Doha.
After visiting Turkey, the emir is due to visit Berlin tomorrow for talks with German Chancellor Angela Merkel, his first trip to a western capital since the crisis began.
Erdogan in July embarked on a regional tour of the Gulf countries, with visits to Saudi Arabia, Kuwait and Qatar in a bid to defuse the crisis.
Yesterday, Kuwaiti Prime Minister Sheikh Jaber al-Mubarak al-Sabah met with Erdogan at his presidential palace.
Over the last years, Qatar has emerged as Turkey's number one ally in the Middle East, with Ankara and Doha closely coordinating their positions on a number of issues including the Syria conflict where both are staunch foes of President Bashar al-Assad.
Ankara has built a military base in Qatar and reportedly already deployed around 200 troops there. The closure of the base was one of the conditions laid by the Saudi-led bloc for the lifting of the sanctions, which was rejected by Doha.
Erdogan has carefully worked to improve Ankara's relations with Riyadh which took a blow over the 2013 ousting of president Mohamed Morsi in Egypt, a close ally of Ankara.
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