Macron, during a visit to Dubai on Thursday, said he was "very concerned" by Tehran's missile program after Saudi Arabia claimed it intercepted a missile fired from Yemen last month.
Referring to the Saudi claim, the French president had raised the prospect of possible sanctions with regard to those activities.
Iran's Foreign Ministry Spokesman Bahram Qassemi said its missile program was defensive and unrelated to the landmark nuclear deal that put a cap on Iran's nuclear activity in exchange for sanctions relief.
"France is fully aware of our country's firm position that Iran's defense affairs are not negotiable," said Qassemi, ruling out the possibility of any talks.
Obama's successor, Donald Trump, decertified the deal last month and slapped sanctions on Iran's powerful Revolutionary Guard Corps. The fate of the deal has fallen on the US Congress, which has 60 days to re-impose nuclear sanctions.
"We have told French officials repeatedly that the nuclear deal is not negotiable and other issues will not be allowed to be added to it," Qassemi said, according to a statement on the ministry's website on Sunday.
France has been trying to save the nuclear deal which Iran signed with six world powers - Britain, China, Germany, France, Russia and the United States.
Last month, Macron told Iranian President Hassan Rouhani in a phone call that France remained committed to the deal but stressed on the necessity to have a dialogue with Iran on other strategic issues, including Tehran's ballistic missile program, a proposal ruled out by Iran.
The US says the missile fired at Saudi Arabia was supplied by Iran. Washington has also called for the UN to hold Tehran accountable for violating two UN Security Council resolutions.