Iran has expressed anger at Morocco's decision to cut off diplomatic ties with the Shi'ite country.
Rabat's accusations that Iran is interfering with Morocco's domestic affairs are "baseless" and "unfounded," and harm unity among Muslims, Iran's Foreign Ministry said.
Morocco announced on Friday it was freezing its diplomatic relations with Iran over Sunni-Shi'ite tensions.
Iran emphasized that the severing of ties at this time would harm Muslim unity and affect support for and solidarity with the Palestinians.
Morocco recalled its charge d'affaires from Iran at the end of February for consultations, demanding Iran explain what Morocco called Iran's unacceptable language after Morocco expressed solidarity with Bahrain.
Bahrain, a small country in the Gulf, which has a Shi'ite majority but is ruled by Sunnis, has become the center of this recent conflict. Last month, a senior Iranian cleric said Bahrain used to belong to Iran, causing tension between Iran and much of the Sunni world.
Many Sunni countries, Morocco included, expressed solidarity with Bahrain after Iran questioned the country's sovereignty.
Iran later backtracked on the comments in an attempt to cool tension, stressing it respected Bahrain's sovereignty.
Morocco also alleges Iranians are propagating Shi'ism among the mostly Sunni population.
The recent spat magnifies Sunni-Shi'ite tension in the Muslim world, and especially between Sunni countries and Iran.
Sunnis are concerned about the prospect of Iran becoming a nuclear power, even though Tehran swears that its controversial nuclear program is for the peaceful purpose of creating energy and not, as many Western countries believe, to manufacture nuclear weapons.
Saudi Foreign Minister Sa'oud Al-Fei'sal said last week that Arabs should form a joint strategy to deal with what he called the Iranian challenge.
Around 15 percent of Muslims worldwide adhere to Shi'ism, constituting the second-largest group of believers in Islam after the Sunnis.
The main bone of contention between Sunnis and Shi'ites is the issue of succession to the Prophet Muhammad, who is believed to have died in 632 AD (CE).
Iran has the highest concentration of Shi'ites, with the vast majority of its 70 million-strong population adhering to this branch of Islam. Other Shi'ite concentrations are located in Iraq, Bahrain, Oman, Kuwait, Pakistan and Lebanon.