It would have been nice to have some idea what the product/process was.
And the result of the BRC/1st audit, eg any NCs with respect to the internal audit(s) which was/were carried out. Only one seems likely.
In addition to Tony's quotations might also add from the BRC7 standard's preamble -
Manufacturing units that are newly built or ‘commissioned’ must ensure that systems and procedures in place are compliant
before an initial BRC audit is undertaken. It is at the discretion of the company when they wish to invite a certification body to carry
out an audit; however, it is unlikely that full compliance can be satisfactorily demonstrated at an audit undertaken less than 3
months from commencement of operation.
and also -
The company shall be able to demonstrate it verifies the effective application of the food safety plan and the implementation of the requirements of the Global Standard for Food Safety.
I hypothesize that the auditor’s interpretation of the standard was that a full internal audit demands a total period of > 3 months, regardless of the unknown product/process and any related risk assessment scheme/schedule. Or, if otherwise, that the auditor's risk assessment (somehow) determined 3 months to be inadequate.
If "regardless" was the logic, it might be interesting to know what is considered by BRC to be a minimum total period.
Repeating part of 3.4.1 - There shall be a scheduled programme of internal audits throughout the year ...........
In theory the “shall” implies (to me) that the absolute minimum is 1 year. In practice, presumably only the Guidance will reveal BRC’s viewpoint (or not). And user's experiences.
As an extension of the above, I predict that the answer to the OP's question is NO (assuming the OP referred to "complete" internal audits). The OP's suggestion does not appear to be expressly forbidden by clause 3.4 but is possibly not within BRC's (qualitative?) interpretation of the "effective" requirement of the "Fundamental".
Logically, the answer to the OP should surely have been considered/informed/requested by/to the auditor after the first audit ?