Seyed Mohammed Marandi, from the University of Tehran, told Al Jazeera: "The five-plus-one proposal has a number of ambiguities that the Iranians feel that until they are resolved properly, Iran cannot respond properly to the proposal itself."
The "five-plus-one" powers are Britain, China, France, Russia, the US and Germany - the six countries involved in the negotiations.
"Iran is trying to resolve these ambiguities and I think this letter is part of that process," Marandi said.
No 'clear response'
Iran's "written response" has not been seen as a formal reply to the EU proposals.
A US spokesman said negotiators from the "five-plus-one" were due to hold a conference call on Wednesday to decide their next move.
Gonzalo Gallegos, as US state department spokesman, said: "If we are not going to receive a clear response, a clear message from them, we are going to have no choice but to pursue additional measures."
Elahe Mohtasham, a nuclear specialist from the Foreign Policy Centre in London, told Al Jazeera that Iran's position "hasn't really changed as far as any suspension of its nuclear centrifuge activity is concerned".
"The best bet - in terms of the interests of the West - is to start negotaitons without any precondiditions ... and then in the course of negotations maybe we will be able to get more concessions from Iran," she said.
"Sanctions haven't worked and are very unlikely to work. Any further sanctions would really increase the price of oil and wouldn't benefit the world economy."
The UK had warned that a lack of a positive answer from Tehran by the end of Tuesday would prompt the six powers to ask the UN Security Council to take further punitive measures.
The new deadline was set after Iran ignored a previous demand to respond by last weekend to the proposed package.
The UN has already imposed three sets of sanctions against Iran over the dispute.
Tensions were again heightened on Monday, Iran said it had successfully test-fired an anti-ship missile with a range of 300km that would allow it to close the Strait of Hormuz between Iran and Oman.
General Mohammad Ali Jafari, the commander of Iran's Revolutionary Guards, said: "No enemy vessels would be able to escape it."
Tehran has steadfastly refused to suspend its uranium-enrichment activities, which it says are aimed only at producing fuel for nuclear power production.
Western powers fear the programme is a cover for developing nuclear weapons.