The letter, submitted to the Swiss embassy in Tehran, which handles US interests in the country, was in reaction to a US intelligence report published last Monday which said Iran halted its nuclear weapons program in 2003.
In the correspondence, Foreign Minister Mottaki demanded "explanations over America's espionage on Iran's nuclear case," the IRNA reported.
Mottaki, addressing students at the Amirkabir University of Technology in Tehran, said the letter was delivered shortly after the US National Intelligence Estimate (NIE) was released in Washington, DC.
The report itself, he said, made clear the use of surveillance satellites and other espionage operations, adding "Iran is seriously following up the issue of espionage.
"The United States officially admitted to spying in this report," he was quoted as saying.
'Peaceful nuclear activities'
Mottaki expressed satisfaction with the principal conclusions contained within the report but denied the existence of a military-oriented nuclear weapons program even before 2003.
Mottaki said the US report reflected "the realities of Iran's peaceful nuclear activities" to an extent of 70%, the IRNA reported. He was quoted by the Mehr news agency as saying the other 30% related to activities before 2003 and was "all lies."
According to Mottaki, "Espionage is one of the channels that powerful countries use to gather information on developing nations." He emphasized that the countries that are involved in negotiations with Iran regarding its nuclear program understand that the option of using military force to resolve the issue is not being considered.
In another response to the US intelligence report, Allaeddin Boroujerdi, the chairman of the foreign affairs committee of the Iranian Parliament, said that "Iran never had a nuclear program that was not for peaceful purposes.
"Today it is up to the Americans to explain to international public opinion why they led a psychological war and imposed sanctions on Iran via the UN Security Council despite the fact that they knew that Iran had peaceful intentions with its (nuclear) program and why they intend to refuse Iran its legitimate right to use it nuclear knowledge for peaceful purposes," Boroujerdi said
Reuters contributed to this report