"None of these issues exist in the first step, but they are part of our last step," Abbas Araqchi was quoted as saying by the official news agency IRNA.
He was replying to a question about whether the application of the additional protocol to the nuclear Non-Proliferation Treaty (NPT), which allows unannounced inspections of Iran's nuclear sites, was included in the proposal.
Araqchi had on Tuesday been cited by IRNA as saying the implementation of the additional protocol "does not exist" in the offer.
As it stands now, Iran is only obliged to inform the IAEA three months ahead of transferring fissile material into the nuclear site.
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Iran, a signatory of the NPT, voluntarily implemented the additional protocol between 2003 and 2005 but ceased to apply it after its nuclear case was sent to the United Nations Security Council.
Last month, US Secretary of State John Kerry said acceptance of the additional protocol by Tehran would help to resolve Iran's decade-long nuclear standoff.
He said that the first phase is expected to last six months. It is aimed at "restoring bilateral trust" and "avoiding measures which could aggravate the (political) climate".
Both parties must also pledge to "address the immediate concerns" of the other side, and to resolve disputes through dialogue.
Araqchi said it would take "several rounds of negotiations" to reach an agreement.