Justice V M Pancholi sought replies of the state and the registrar to a petition filed by Kaira Milk Producers Union, seeking to quash the audit.
Government pleader Manisha Lavkumar said that no audit will be carried out till the next hearing on June 11.
Kaira Milk Producers Union is one of the district constituent of Gujarat Cooperative Milk Marketing Federation (GCMMF), which markets its product under the brand 'Amul'.
On May 26, registrar ordered the special audit and formed a team of seven members to inquire into 11 issues pertaining to alleged irregularities in the election.
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This order was issued after representations were made to the Chief Minister and the Minister of the Cooperative Department by two BJP members who were elected in the poll, says the petition.
It argues that an election result can be challenged only through an election petition. Also, inquiry can be ordered under section 86 of the Cooperative Societies act and not section 84(5)(a), as in this case.