Iran says its foreign minister wanted to resign last month after being kept in the dark about a surprise visit by Syria's Bashar Assad to Tehran.
President Hassan Rouhani ultimately rejected Mohammad Javad Zarif's resignation, throwing his full support behind the diplomat who negotiated the country's nuclear deal with world powers. Zarif later returned to his job.
Both men face growing pressure from Iranian hard-liners as the nuclear accord unravels under American pressure.
Foreign Ministry spokesman Bahram Ghasemi said on Tuesday that "one of the reasons for Zarif's resignation was this type of lack of coordination with the Foreign Ministry."
Assad was warmly received by Supreme Leader Ayatollah Ali Khamenei, Rouhani and also Gen. Qassem Soleimani, the commander of an elite unit of the Revolutionary Guard.