Iranian President Hassan Rouhani, who had been at the two-day Istanbul conference along with over 30 other heads of state and government from Islamic countries, did not attend the closing meeting in protest at the criticisms.
"The (Organisation of Islamic Cooperation) Conference deplored Iran's interference in the internal affairs of the States of the region and other Member States including Bahrain, Yemen, Syria, and Somalia, and its continued support for terrorism," said the summit's final statement.
The Arab League declared Iran's ally Hezbollah a "terrorist" group in March after Gulf kingdoms did the same earlier in the month over the movement's support for the Damascus regime in Syria's war.
There was a security lockdown around the summit venue in Istanbul, the former capital of the Ottoman Empire from where Sultans for centuries ruled Muslims from the Balkans to Arabia.
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Turkey's relations with Cairo have still not recovered from the 2013 ousting of Islamist president Mohamed Morsi, a close ally of Ankara, while ties with Amman are being tested by differences over Syria.
Iran's Rouhani is due to meet Turkish President Recep Tayyip Erdogan in Ankara on Saturday.