"The relationship should be at the level of official political, diplomatic and economic channels between the two countries," Hadi said.
"These relations should not be at the level of political parties, groups or militias, regardless of their policies," Hadi added, addressing the new Iranian ambassador to his country who had just presented his credentials.
Hadi was quoted by Yemen's official news agency as saying that Iran was a major regional power that had its own interests, adding that the government and people of Yemen had the power to protect joint interests and investments.
He called on Iran to invest in Yemen and improve relations between the two countries based on international norms.
The news agency quoted the new Iranian ambassador as saying that he was only in Yemen to deal with the Yemeni government.
He said he would work hard to increase cooperation between his country and Yemen, noting that Iran was ready to improve bilateral cooperation.
Iran came under criticism in Yemen soon after the Shiite Houthi movement flexed its political and military muscles by taking over Yemeni capital Sanaa in late September and moved to extend its control to other provinces as well.
The Yemeni government has repeatedly accused Iran of standing behind the Houthis' recent rise to power.