Fonterra is aiming to launch its new Trading Among Farmers (TAF) scheme in November after getting approval from a majority of farmer-shareholders.
Of those who voted, 67% supported the TAF plan.
Final votes were counted at Monday's special meeting of the dairy cooperative at eight venues around the country.
The scheme allows farmers to trade shares among themselves and outsiders to invest in the dividend earning from shares that farmers deposit in a shareholders fund.
Fonterra chairman Sir Henry van der Heyden says the result gives it the mandate it needs to proceed.
But a proposal to tighten up the company's constitution by reducing the size of the shareholders fund in which outsiders can invest, and the number of shares that can be traded, fell just short of the 75% support required.
Sir Henry says that won't stop TAF from going ahead, but Fonterra's board supports having those tighter conditions and will try again to get farmer backing for the changes later this year.
"We will take that resolution back to our shareholders at the annual meeting ... which will be later on this year."
Federated Farmers' dairy chair Willy Leferink says a two-thirds majority vote is a convincing result and he supports the board's intention to persist with constitutional changes.
Mr Leferink hopes that will help to reassure farmers who opposed the plan because of the shareholders' fund and its accessibility to outside investors.
He said the issue has divided the cooperative and "it's now up to the board to unify the co-op again."
One of the most vocal farmer critics of TAF, Lachlan McKenzie, thinks the board will have its work cut out to ease opponents' concerns and restore unity to the co-operative.
"We don't think the board has a very clear mandate," he says. "One in three farmers do have concerns".
Fonterra has said that if the fresh vote on tighter conditions fails at the November annual meeting, the measures will still become board policy.
Opposition calls for legislation on fund size
Opposition political parties want restrictions on the size of Fonterra's proposed shareholders fund to be built into legislation.
Labour Party primary industry spokesperson Damien O'Connor says Fonterra farmers have been left with the worst of both worlds and they need legislative protection in the Dairy Industry Restructuring Amendment Bill going through Parliament.
Mr O'Connor says the protections are critical and the legislated size limit is needed - though he does think a 20% limit will be approved in a second vote.
Green Party agriculture spokesperson Steffan Browning says the TAF plan will put smaller family-scale farmers at risk.
He says allowing non-farmer investment through the proposed shareholders fund will put pressure on the Fonterra board to increase the return to investors through dividends, at the expense of farmers' milk payments.
Mr Browning says the dairy industry legislation paving the way for TAF is flawed and needs to go back to the Primary Production Select Committee.
However, Primary Industries Minister David Carter says the Government is satisfied with the two-thirds majority vote for TAF and he sees no need for legislative controls on the share-holders fund.
Mr Carter says the only changes the Government is proposing to the Dairy Industry Bill are some technical amendments.
The Bill is part way through its second reading Parliament, whichi s expected to be completed on Tuesday night. It will then go to committee stages for a clause by clause consideration by MPs before coming back for its third and final reading.