A foreign ministry statement said the Comoros viewed Tehran as "interfering" in "the internal affairs of certain countries" and "not respecting diplomatic conventions".
Relations between majority Shiite Iran and Sunni Saudi Arabia dived after the January 2 ransacking of the Saudi embassy in Tehran and the Saudi consulate in Mashhad, Iran's second city.
The ransacking came amid anger over Riyadh's execution of Nimr al-Nimr, a prominent cleric from the kingdom's Shiite minority.
Following the execution Jeddah severed diplomatic relations with Tehran.
Comoros' foreign ministry said it had called on the Iranian ambassador to clear his desk.
The move came a week after the Comoros recalled its own ambassador from Tehran judging that Iran has created a climate of "gratuitous aggression" towards Jeddah.
"One cannot violate with impunity the sovereignty of diplomatic missions," the ministry's director general Ahamada Hamadi told AFP, referring to the ransacking.
The three islands of Anjouan, Grand Comore and Moheli that make up the Comoros have a total population of just under 800,000 people, nearly all of whom are Sunni Muslims.
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