The envoy, Yunus Demirer, heard the Iraqi complaint on Sunday after several days of charge and counter-charge.
Erdoğan accused his Iraqi counterpart Nuri al-Maliki on Thursday of stoking conflict between Shi'ite Muslims, Sunni Muslims and Kurds through "self-centred" behaviour.
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 neighbour Syria may lead to a wider Sunni-Shi'ite conflict in the region.
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.
"(Foreign ministry undersecretary) Mr. Labeed Abbawi acquainted the Turkish Ambassador with the Iraqi government's intense protest against the recent statements," the Iraqi foreign ministry said on its website.
"Undersecretary Abbawi expressed hope that the Turkish government will stop giving statements that affect Iraq's sovereignty and internal affairs."
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.