The 15-member committee spent weeks reviewing the text of the July 14 agreement, known as the Joint Comprehensive Plan of Action (JCPOA), for what it said could be breaches of negotiators' "red lines".
The panel had largely been sidelined over its ability to influence the accord's fate although its report paves the way for a formal vote in parliament.
A law passed earlier this year gave final oversight of the nuclear deal to Iran's Supreme National Security Council (SNSC), rather than lawmakers, many of whom have railed against the agreement.
In their report the lawmakers hit out at the decision to allow inspections of military sites, which supreme leader Ayatollah Ali Khamenei had appeared to rule out in a speech just weeks before the deal was sealed.
"It is evident that, based on the JCPOA, access to Iranian military sites has become possible," the panel said.
"The JCPOA has serious weaknesses in the security section. Unless there's a revision regarding the inspection of military, defence and security sites, it will cause problems for the country.
The lawmakers, however, said the review made "the assumption that Iran's negotiating team had enjoyed the supreme leader's trust" during the talks that led to the deal and its passing would see sanctions lifted.
Khamenei has the last word on all policy matters in the Islamic republic as his authority trumps Rouhani and all politicians. His speeches often backed the negotiators but stopped short of endorsing the deal.
The panel further criticised the agreement with Britain, China, France, Russia and the United States plus Germany, saying Iran's obligations were "clear and explicit" whereas the West's obligations were not so.
In particular the placing of restrictions on some aspects of Iran's nuclear activities for 15 years was "a serious shortcoming".
Under July's accord Iran will place limits on its nuclear programme for at least a decade in return for the lifting of all nuclear-related UN and international sanctions.
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