Hossein Amir Abdollahian told Wolfgang Bruelhart, Switzerland's top diplomat for the Middle East, the claims were "thoroughly baseless" during talks in Tehran.
"The Islamic Republic of Iran firmly believes that the only solution to the Yemeni crisis is through political talks and pursuit of peaceful approaches and respecting the decisions of Yemeni people," he said.
There have been a number of unproven claims in recent months that Iran sent weapons to Yemen's Houthi rebels.
In October, Reuters cited unnamed Iranian and American sources saying that Iran was sending weapons via Oman.
Oman's foreign minister denied the story, saying he was prepared to "clarify any suspicions if they arise."
The story broke after Yemen's army chief of staff, Mohammed al-Maqdishi, said Oman needed to be "a lot stricter" about smuggling across its borders.
The following month, a Conflict Armament Research (CAR) report suggested that smuggled weapons found in the waters between Somalia and Yemen - coupled with weapons found in Yemen - "probably originated in Iran".
The research found the weapons' serial numbers were in sequential order, suggesting "the rifles derived from a national stockpile".
"The weight of evidence point[s] to Iran as the original source," the report stated.
A CAR researcher stood by his company's claims, saying there was "clear evidence" that Iran had sent weapons to the Yemeni rebels.
"Either the Government of Iran is complicit in the supply of weapons to Yemen or they are experiencing high-level corruption within their military structure by people with the ability to pillage large amounts of materiel from national stockpiles," said CAR field investigator, Tim Michetti.
"Neither of which I imagine they'd be happy admitting."
Abdollahian criticised the Saudi-led aggression in Yemen, saying it was the main cause of violence in the region.
"The presence of various terrorist groups in the south of Yemen - which are on the rise due to the war and conflict in the country - is not only a threat to the security of the region but also a highly worrying issue for the security of international waterways," he said.
Abdollahian has previously made public statements with regards Hizballah's role in the region - another group with proven ties to Iran.
"We are proud of Lebanon's Hizballah as the vanguard of resistance against the Zionist regime and the champion of the fight against terrorism in the region," Abdollahian told Iran's official IRNA news agency.
Peaceful demonstrations calling for the downfall of the Saleh regime in 2011 were met with violent and often brutal responses. was given immunity and removed from power and was replaced with current President Abd Rabbo Mansour Hadi.
In September 2014, the Tehran-backed Houthi rebels aligned with the previous president - Ali Abdullah Saleh - to bring down the new transitional government in Sanaa, following months of protests.
In March 2015, a Saudi-led coalition launched a military campaign to help the internationally recognised government regain control of territory lost to the Houthi rebels.
Figures suggest more than 10,000 people, half of which are civilians, have died since this intervention, while 3 million more were forced into displacement.