"We know that they are trying to develop nuclear weapons, we know their real intentions," he told reporters in Berlin after talks with German Foreign Minister Joschka Fischer, who had briefed him on a recent visit to Iran.
Shalom said he hoped that the IAEA would decide later this month to begin unfettered inspections around Iran.
"We will be very happy if (the IAEA) will give free access to the inspectors ... to look at these nuclear stations that are located in Iran, all of them, the civil ones and the military ones," he said.
The UN nuclear watchdog, has set a deadline of October 31 for Tehran to allow tougher inspections of its nuclear programme, amid fears it may be secretly developing atomic arms. Iran fiercely denies the allegations.
Shalom maintained that the regime in Tehran is still hostile to Israel and continued to send missiles to the Lebanese Shiite militia group Hezbollah.
"The only threat from Iran is toward Israel. If they are going to use any time in the future any nuclear weapons it will be against Israel," he said.
"Imagine what will happen ... when they have nuclear weapons and if there is an even more radical regime at that time," he added.
Fischer and his counterparts from Britain and France made Tuesday an unprecedented joint mission to Iran, during which they won a series of concessions from the Islamic regime.
Iran announced it would sign a protocol to a non-proliferation treaty which will allow the International Atomic Energy Agency (IAEA) to carry out surprise visits to suspect facilities.
Tehran also promised "full transparency," and reiterated its commitment to the treaty and said it would suspend all uranium enrichment and reprocessing activities.