Israel and world Jewish groups have denounced the pact which is seen as running counter to U.S.-led efforts to isolate Iran over its disputed nuclear program.
Argentinian authorities secured Interpol arrest warrants in 2007 for five Iranians and a Lebanese for the killing of 85 people in the Argentinian Jewish centre (AMIA).
Iran denies any link to the attack.
Argentina said last month it had agreed with Iran to establish a "truth commission" made up of five foreign legal experts to review all the relevant documentations of the attack, which Argentine courts accuse Tehran of sponsoring.
Iran's foreign minister said on Tuesday his country was committed to the accord.
"We have signed a memorandum of understanding with Argentina to resolve the AMIA case and both sides are committed to its contents," the official IRNA news agency quoted Foreign Minister Ali Akbar Salehi as saying during a visit in Moscow. "This MOU sets the base for our handling of the AMIA file," he said.
Argentinian President Cristina Fernandez, who has close ties with other Latin American leaders who are on good terms with Tehran, such as Venezuela's Hugo Chavez, has hailed the agreement as historic.
According to a document posted on Fernandez's Facebook page, the agreement plans for Argentine legal officials to meet in Tehran to question "those people for whom Interpol has issued a red notice".
Iranian Defence Minister Ahmad Vahidi is among the Iranian officials sought by Argentina, which is home to Latin America's largest Jewish community.
But Iranian Foreign Ministry spokesman Ramin Mehmanparast denied Iranian officials would be questioned over the bombing.
"This report is a lie," Mehmanparast told a news conference in Tehran reported by the Iranian Students' News Agency (ISNA).
Julian Dominguez, the head of the lower house of Congress and a government ally, said senators would start analyzing the bill containing details of the accord on Wednesday.
Julio Schlosser, president of Argentina's DAIA Jewish community group, said Iran's refusal to allow its officials to be questioned was predictable.
"This is what we expected from the start. We said that Iran was not a reliable negotiator," Schlosser told local radio. "This is the cherry on a cake that we refused to eat. The outcome was already clear," he said.
Argentinian officials were not immediately available to comment on the statement by Mehmanparast.
(Reporting by Zahra Hosseinian and Helen Popper; Editing by Jon Hemming)