Reported by the BBC Iran's island offices condemned:
Abu Musa and the Greater and Lesser Tunb islands are controlled by Iran but claimed by the United Arab Emirates (UAE) with broad Arab support.
Iran says the two administrative offices on Abu Musa are to help ship registration and maritime rescue.
The GCC statement interfered with its internal affairs, a spokesman said.
Correspondents say the GCC fears the move will give Iran greater control of shipping traffic through the Strait of Hormuz, the waterway used by tankers carrying oil from the Gulf out into the open sea.
Iran took control of the islands in 1971 when Britain granted independence to its Gulf protectorates.