Mottaki had left Tehran on Tuesday but his plane was forced to turn back from Baghdad because of high winds and dust storms, Zebari told AFP.
The two neighbours agreed in January to establish a high-ranking joint committee to improve cooperation and the "routine" trip of several days was part of that process, he said.
The two Shiite-majority countries fought a 1980-1988 war in which around one million people died. Ties have warmed considerably since the overthrow of Saddam Hussein's Sunni-dominated regime by US-led forces in 2003.
Iraqi Prime Minister Nuri al-Maliki visited Tehran last month to seek Iran's help in rebuilding the war-torn country.
