The order to this effect was issued today by State Registrar of Cooperative Societies, Nalin Upadhyay.
Though the order was issued today, it will be implemented only after four weeks given the Supreme Court directive.
The SC had passed an interim order in March saying that if government passes any adverse order against Chaudhary, it should be implemented only after four weeks.
"Through this (today's) order, Chaudhary is now barred from holding any position in any cooperative society as well as from contesting polls in such societies for a period of six years," said Upadhyay.
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In March 2015, he was sacked as chairman of Mehsana-based Dudhsagar dairy on the charge of alleged irregularities.
Chaudhary had then been disqualified from contesting elections to any cooperative society or from holding any post for three years by the cooperative registrar, following which he challenged the order in Gujarat High Court and then in the apex court.
The SC had then granted Chaudhary an interim relief stating that any adverse order against him should be implemented only after four weeks.
"This new order will be implemented as per Supreme Court's directive after four weeks. Now, this new order, having a period of six years, will replace our old order, which disqualified him for three years," added Upadhyay.