Iran appears to blame Saudi Arabia after repatriated Yemen envoy dies of Covid-19
Ambassador Hasan Irlu "was evacuated in poor condition due to delayed cooperation from certain countries," ministry spokesman Saeed Khatibzadeh told state media, without naming any country.
A Saudi-led coalition intervened in Yemen in 2015 against the Iran-aligned Houthis after the movement ousted the internationally recognised government from Sanaa, the capital.
The coalition has imposed a sea and air blockade on areas the group controls, including flights from Sanaa.
The Saudi government media office did not immediately respond to a Reuters request for comment.
Saudi Arabia and Iran launched direct talks this year at a time when global powers are trying to salvage a nuclear pact and as UN-led efforts to end the Yemen war stall.
Khatibzadeh honoured Irlu as a "martyr" and said he was a survivor of chemical attacks in the Iran-Iraq war in the 1980s.
"We have lost a great friend," Houthi deputy foreign minister Hussein al-Ezzi said, offering condolences on Twitter.
Last December, the US Treasury blacklisted Irlu and described him as an official of Iran's elite Quds Force, the overseas arm of Iran's Revolutionary Guards, and a pillar of Iranian efforts to project its power in Yemen, Syria, and elsewhere.
Two Yemeni political sources close to the Houthi movement and a foreign source told Reuters that Irlu had recently kept a low profile due to illness and political tension.
The Yemeni sources said some Houthi leaders had resented perceived "interference" by Irlu.