FRUIT and vegetable wholesalers are waiting on details of rent options for the new market at Epping.

A ballot was held last week to determine which stores they would operate from, despite legal advice and attempts to postpone it on the grounds it was unfair, biased and lacked transparency.

During a two-hour meeting the day before, wholesalers agreed to co-operate with each other to ensure leaseholders who traded under the same business name were able to choose adjacent stores at the new site.

Freshstate chief executive John Roach said the decision was made to allow the ballot go ahead under protest, with a written warning to Minister for Major Projects Denis Napthine that anomalies that had not been addressed, might be raised at a later time.

After three hours and eight ballots the 74 large stores, 30 medium stores and 40 small stores were finally allocated under the supervision of an independent expert and a probity adviser.

Wholesalers are now awaiting information on rent options for the new sites and a call for expressions of interest for stands on the trading floor.

Ballots for fruit and vegetable standholders and flower market standholders will be held early next year.

Mr Roach said no one had missed out in last week's ballot.

''Everyone who had a holding here (at Footscray Road), got a holding there,'' he said.

''And people who got less space will be paid the equivalent of $3000 per square metre (in compensation).''

Freshstate, which represents Melbourne Market wholesalers, last month wrote to Minister for Major Projects Denis Napthine expressing concern about a lack of information on issues of space gained or lost, inconsistencies between proposed trading stand size and the total number of stands, and the change from five ballots to eight.

Storeholders are expected to have access to their new sites in July next year - 10 years after it was decided the wholesale market should move out of Footscray.

Dr Napthine said many of the businesses present at the ballot had a long and intergenerational history and were involved in the 1968 ballot when the market moved from the Queen Victoria Market site to the current facility at Footscray.

Melbourne Market Authority chairman Neil Lowe said the process of consultation with market stakeholders, including wholesalers, growers and retailers, was ongoing.

''There has been a very active consultation program run by the Melbourne Market Authority in co-operation with the Department of Business and Innovation on relocation issues and this will continue until the new market opens and beyond,'' he said.