Seven other Iranians with international arrest warrants against them also will also be questioned by the Argentine judge in Tehran, Argentine Foreign Minister Hector Timerman confirmed on a local radio station.
But he emphasized: "I made sure (Iran Defense Minister Ahmad Vahidi) will have to be present when the judge questioned them and he will be."
Argentina has long accused Iran of masterminding the deadly attack and since 2006 has sought the extradition of these eight Iranians, who also include former president Akbar Hashemi Rafsanjani and former foreign minister Ali Akbar Velayati.
Iran has always denied any involvement in the bombing, in which 85 people died, and has refused to arrest the suspects.
On Sunday, after months of negotiations, Argentine President Cristina Kirchner announced that her country and Iran had agreed to create a "truth commission" with five independent judges -- none of whom can come from either Iran or Argentina -- to investigate the bombing.
She said that under the agreement, Buenos Aires might finally be able to question the Iranian suspects.
Argentine Judge Rodolfo Canicoba Corral and prosecutor Alberto Nisman, the lead investigator into the attack, will go to Tehran to take the Iranians' testimony.
"Maybe these interrogations will bring new evidence to the surface or suggest new avenues" of investigation," Timerman said, adding that the judicial inquiry has been stalled for years.
The foreign minister also denied that Venezuela, which has good relations with both Iran and Argentina, had any influence on the deal, saying it was reached through direct dialogue between himself and his counterpart in Tehran.
The negotiations have been criticized by Israel and Argentina's 300,000-strong Jewish community, the largest in Latin America.
Both have demanded there be no let-up in the Argentine authorities' efforts to put the Iranian suspects on trial.
This week, Israel's foreign ministry protested the agreement to Argentina's ambassador at a meeting in Jerusalem.