He said that the fighting in north Yemen between government forces and the Houthis, who are from the Zaidi sect of Shia Islam, can be resolved by "collective efforts".
"It can restore security, peace and tranquillity among the people of Yemen and the whole region.
"Any measure in contrast of such approach will serve the enemies of Islamic and Arab states. We believe that any approach other than this will not serve the interests of regional nations."
Yemen later responded to the comments, rejecting any outside interference.
"We welcome what Mottaki affirmed about Iran's position towards Yemen's unity and stability, and Yemen reaffirms that it definitely rejects the interference in its internal affairs by any party," an official in the Yemeni foreign ministry said.
The Houthis have been fighting for the last four years for a return to autonomous rule. The group has said that they have been economically and politically marginalised by the Yemeni government in Sanaa.
Attacks by both sides have escalated since August and this week Saudi Arabia, Yemen's northern neighbour, launched an offensive against the Houthis on the border between the two countries.
Hasham Ahelbarra, Al Jazeera's correspondent reporting from north Yemen, said the Yemeni government on Wednesday claimed to have attacked northern Houthi targets, killing dozens of opposition fighters.
He said that Yemen has deployed the coast guard along the northwestern coast "because that area is extremely strategic and they have concerns that the Houthis might get shipments of weapons from arms smugglers or different parties to continue fighting the Yemeni government".
The offensive followed the killing of a Saudi border guard in a raid by the Houthi fighters.
Saudi naval forces have also imposed a naval blockade in the Red Sea which they say is aimed at stopping the flow of weapons to rebels.
In his comments on Wednesday, Iran's foreign minister insisted that regional nations should "seriously hold back from intervening in Yemen's internal affairs".
"Those who pour oil on the fire must know that they will not be spared from the smoke that billows," he said.
Sana'a has previously accused Iran of supporting the Houthis, whereas one of the Houthis' complaints against the Yemeni government is its closeness to the Saudis.
Speaking to Al Jazeera, Hossein Shobokshi, a columnist with the Arabic Asharq Alawsat newspaper, was also critical of Iran's offer to help.
"It is a very odd situation that Iran threatens anybody that interferes in Yemeni affairs. This is an internal issue between the Yemenis. Saudi Arabia is protecting its borders," he said.
"What business does Iran have stating what it has stated?
"But it also falls in sync with what Iran has been doing. Interfering in other countries' affairs - we have seen it in Jordan, Sudan, Palestine, Egypt, Bahrain, Kuwait, and Iraq - creating pockets of influence and trying to control its puppets in every part of the Arab world."
Shobokshi said there needs to be "a collective effort to sit around a table, to, once and for all cut the cords aiding the Houthis and bet on an internal, stable form of government in Yemen because this will help everyone at the end of the day".