Under the agreement, Tehran agreed to limit its disputed nuclear programme in return for the easing of economic sanctions.
The Iranian nuclear deal should be altered to prevent Iran's development of ballistic weapons, Prime Minister Benjamin Netanyahu indicated on Sunday, the same day Iran's president vowed to continue with his country's ballistic-missile development.
The Sunday report by the semi-official ILNA news agency quotes ministry spokesman Bahram Ghasemi as saying "an intention was expressed by the American side that was not approved by President Rouhani", in reference to the alleged meeting request.
Iranian president lashes out at United States and says he does not believe Tehran's missile programme violates global laws.
Amid the possibility of the US' unilateral withdrawal from the Iran nuclear deal, also known as JCPOA (Joint Comprehensive Plan of Actions), and new anti-Tehran sanctions, Iranian President Hassan Rouhani has outlined his position on the issue.
He has also said Tehran has broken the "spirit" of a 2015 landmark nuclear accord in which Iran agreed to curtail its nuclear activities in exchange for relief from worldwide sanctions.
The United States has already imposed unilateral sanctions on Iran, saying its missile tests violate a UN resolution, which calls on Tehran not to undertake activities related to missiles capable of delivering nuclear weapons.
"Part of the (Ballistic Missile Defence Review) is to try and figure out how much of a threat Iran is, and what more we may need to do beyond what we have right now", one Pentagon official with knowledge of the planning told Foreign Policy.
"Unfortunately, Reuters distorted what Mr. Amano said about Iranian military sites and created a media hype while what Amano said was that there was no military subject mentioned in the JCPOA", said Behrouz Kamalvandi, Deputy Head of the Atomic Energy Organization of Iran (AEOI) for International Affairs on Saturday.
However, Iran has underscored that they will never agree to such terms.