"Actually, throughout, we have had good relations with Iran and we believe that the security and stability of Afghanistan are also in the interests of Iran," Abdul Rahim Wardak told the Associated Press.
On Wednesday, U.S. Undersecretary of State Nicholas Burns said in Paris that Tehran was directly supplying weapons to the Taliban. He told CNN television there was "irrefutable evidence" that arms shipments were coming from Iran's government.
The State Department later appeared to step back from Burns' assertion, but stressed that the United States has proof that weapons from Iran were reaching Taliban fighters in Afghanistan.
Tehran has denied the accusations. Wardak, who is attending a NATO defense ministers' meeting in Brussels, also played down suggestions that Iranian authorities were sending arms shipments to the Taliban.
"There has been evidence of weapons, but it is difficult to link it to Iran," Wardak said. "It is possible that (they) might be from al Qaeda, from the drug mafia or from other sources."
The majority of weapons captured from the insurgents have been of Soviet origin, but arms from East Germany, China and Egypt have also been seized, he said.
U.S. Defense Secretary Robert Gates, who is attending the Brussels meeting, also mentioned the alleged weapons transfers from Iran.
"The irony is the Afghan government and the Iranian government have pretty good relationships," Gates told reporters. Gates, who was in Afghanistan last week, said Afghan President Hamid Karzai talked to him about the good relationship the two countries have.
Gates speculated that Tehran may be "trying to play both sides of the street, hedge their bets."
In a wide-ranging interview with the AP, Wardak said he would appeal to the defense ministers of NATO and allied countries to provide greater assistance in training Afghan security forces.
He said the establishment of an effective Afghan air force was a top priority because air support would enable the army to conduct independent operations without having to rely so heavily on the international forces.
Afghanistan currently operates a handful of Czech-built L-39 jet trainers, together with some old Soviet Mi-17 helicopters and Antonov An-26 twin-engine transports.
"We have all agreed that the only sustainable way to secure Afghanistan is to enable the Afghans themselves to defend the country as they have done for thousands of years. Based on that I would like to have further acceleration of the Afghan national security forces both in numbers and capabilities," Wardak said.