After meeting Karel De Gucht, the Belgian foreign minister, Mottaki said on Monday: "We believe the time of threats is over.
"There is still time for all the parties to reach a compromise and I hope they use that time.
"The Security Council of the United Nations should not be considered as a tool in the hands of some countries."
Mottaki spoke amid fresh diplomatic efforts to defuse the crisis, and as an Iranian negotiating team was in talks in Russia about a compromise proposal to enrich uranium on Russian territory.
Iran maintains that it wants only to generate electricity with its nuclear programme, but some of its activities have raised concerns in the West that it is trying to develop an atomic weapon.
Mottaki said he was in Brussels to clarify Iran's stance, as a signatory to the nuclear Non Proliferation Treaty (NPT), to the European Union.
"Europe needs to have a new picture to move realistically to the facts," he said.
Talks are on for a compromise
deal to enrich uranium in Russia
He said that two scenarios were possible - either to leave the problem to fester, or to negotiate to try to balance concerns about the Islamic republic's nuclear programme and Tehran's rights as an NPT signatory.
"If we leave it, something will happen," he said.
A source close to Javier Solana, the EU's foreign policy chief, who was due to meet Mottaki later on Monday, said the EU would urge Iran to move back to the diplomatic track but that there would be no negotiations.
De Gucht, in a strongly worded statement, voiced scepticism that Iran was only trying to develop nuclear energy.
"It is very difficult to believe that there is not a military aspect to Tehran's atomic programme," he said.