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Comptroller general Marta Acosta Zúñiga, before the legislative assembly's public spending committee, "reaffirmed" questions her office had asked about the planned overhaul.
The comptroller's office previously invalidated a project study amid allegations of irregularities.
There needs to be greater technical, financial and legal scrutiny to guarantee the success of a project of this size, an assembly report quoted Acosta as saying.
Acosta said it was "worrying" that the project has been on hold since 2013. She added there is no clarity regarding the financial contributions made by Recope and CNPCI because it is still not clear whether the project will continue.
Recope head Sara Salazar is scheduled to appear before the committee.
According to preliminary information, the US$1.5bn modernization project aims to increase capacity to 65,000b/d from 25,000b/d, and produce cleaner products.
UPCOMING BNAMERICAS EVENTS
5TH Mexico Infrastructure Summit
4TH Mexico Oil & Gas Summit