Greek Foreign Minister Nikos Kotzias has submitted his resignation, Greece's Skai TV reported on Wednesday.
Earlier, it had been widely reported Kotzias had clashed with Defence Minister Panos Kammenos over a deal brokering an end to a decades-old name dispute with Macedonia. Kotzias was Greece's main negotiator in the talks that led to the June accord with Skopje to rename the neighboring country North Macedonia.
Prime Minister Alexis Tsipras took over as foreign minister on Wednesday and said he would not let personal agendas overshadow policy.
Tsipras said he would do whatever was needed to ensure the success of an accord with Greece's neighbor to end a decades-old dispute over its name.
Tsipras said of assuming the foreign minister role: "It is a decision not to tolerate, from now on, any double-speak from anyone, or any personal agenda in the national line of the country."
He said he was "pained" to have to accept the resignation of Kotzias.
The name deal has however been thrown in limbo following a referendum in Macedonia on Sept. 30 which failed to muster a minimum turnout to render it valid.
Greek media reported on Wednesday that Kotzias and Kammenos, a coalition partner in the government, had argued during a cabinet meeting on Tuesday chaired by Prime Minister Alexis Tsipras.
Kammenos, who heads the small right-wing Independent Greeks party, is vehemently against the accord with Macedonia and has said he could quit the government over it.