The envoy, Yunus Demirer, heard the Iraqi complaint on Sunday after several days of charge and counter-charge.
Turkey, in turn, summoned the Iraqi charge d’affaires Sudat Khidir on Tuesday and told him that the latest statements by Iraqi officials condemning Turkey is unacceptable.
Foreign Ministry officials told the Iraqi envoy that Iraq’s peace and stability is a priority matter for Turkey as the situation in Iraq would have direct repercussions on Turkey.
Erdoğan accused his Iraqi counterpart Nouri al-Maliki on Thursday of stoking conflict between Shi'ite Muslims, sunni Muslims and Kurds through "self-centred" behavior.
Maliki fired back that Turkey was becoming a "hostile state" with a sectarian agenda, saying it was meddling in Iraqi affairs and trying to establish regional "hegemony".
Erdoğan returned to the fray on Saturday, saying: "If we respond to Mr. Maliki, we give him the opportunity to show off."
Analysts say mainly Sunni Turkey is worried that growing tensions in Iraq and violence in their mutual neighbor Syria may lead to a wider Sunni-Shi'ite conflict in the region.
Turkish officials also conveyed a message to Iraq during the meeting, saying that Iraqis are brothers of Turks and that Turkey is rejecting sectarian- and ethnic-based policies in the war-torn country.
Turkish diplomats also told the Iraqi envoy that Turkey strongly rejects summoning of Turkish ambassador to Baghdad on Sunday.
Erdoğan's government has also recently forged close ties with Masoud Barzani, president of Iraq's semi-autonomous Kurdish region, which is embroiled in a row with the Baghdad government over claims to the city of Kirkuk and the region's oil.
Erdoğan has criticised Maliki several times since sectarian tensions flared in Iraq in December when the Shi'ite-led government tried to remove Sunni Deputy Prime Minister Saleh al-Mutlaq and sought an arrest warrant for Sunni Vice President Tareq al-Hashemi on charges he ran death squads.
Hashemi fled Baghdad and has since met Erdoğan in İstanbul.
The rift between Baghdad and the Kurds worsened this month when the Kurdistan Regional Government said it was halting oil exports because the central government was not paying oil firms operating in the north.
Iraq is Turkey's second largest trading partner after Germany, with trade reaching $12 billion last year, more than half of which was with the Kurdish region.