A foreign ministry statement said the Comoros viewed Tehran as "interfering" in "the internal affairs of certain countries" and "not respecting diplomatic conventions".
Iran bans all products from Saudi Arabia after ties cut
Comoros' foreign ministry said it had called on the Iranian ambassador to clear his desk.
The move came a week after the Comoros, a member of the Arab League, recalled its own ambassador from Tehran judging that Iran has created a climate of "gratuitous aggression" towards Riyadh.
Relations between majority Shia 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 Shia minority.
Following the execution Riyadh severed diplomatic relations with Tehran.
Several Arab countries followed suit and severed or reduced relations with Iran.
"One cannot violate with impunity the sovereignty of diplomatic missions," the Comoros foreign ministry director general Ahamada Hamadi told AFP, referring to the ransacking.
Don’t snub the Saudis
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.
Since gaining independence from France in 1975, the impoverished archipelago has witnessed more than 20 attempted coups, four of which were successful, but it has enjoyed relative stability in recent years.
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