Store workers for one of Australia's biggest supermarkets have voted in favour of a new pay deal, after a campaign plagued by allegations of "misinformation" and "bad faith bargaining".

The vote by almost 100,000 workers at Woolworths was one of the largest Enterprise Bargaining Agreement (EBA) votes in history, and saw 62 per cent come back in favour of the four-year deal.

The deal, which is now subject to approval by the Fair Work Commission, covers the pay and entitlements of more than 130,000 workers inside Woolworths supermarkets and fulfilment centres.

"We're very pleased our new enterprise agreement [has] received a majority yes vote," a company spokesperson said.

The union that represents at least 70,000 Woolworths workers also advocated for the deal, with the Shop Distributive and Allied Employers' Association (SDA) sending text messages to members in the last week encouraging them to vote yes.

"Vote yes for better wages, improved rostering, and stronger rights at Woolworths," a text message sent to one Woolworths worker in the hours before the vote closed on Wednesday evening read.

The SDA's national secretary, Gerard Dwyer said he's "very pleased" that 62 per cent of voting workers decided to take the deal.

"This is a good agreement," Mr Dwyer said.

"It provides a whole range of additional benefits, a really superior package for part-time members. 

There's something in it for everyone."

But a much smaller union that represents less than 1,000 of the supermarket's workers said their workforce just voted for a dud, and the result shows that many of them knew this.

"Thirty-six thousand of them voted no," Retail and Fast Food Workers Union (RAFFWU) secretary Josh Cullinan said.

"That should ring alarm bells for the SDA and Woolworths."

What is controversial about the deal?

Many of Woolworths' workers are covered by the industry award for General Retail Industry, which currently gives a minimum hourly rate of $24.73 per hour for an entry level worker.

Woolworths' expiring agreement gives those workers 39 cents above that minimum or $25.12 per hour.

From July 1, the award is going up to $25.65 per hour, in line with the Fair Work Commission's decision to legally raise the minimum wage for millions of Australian workers by 3.75 per cent.

The base wage just offered up by Woolworths and voted in favour of by its workers will give them $26.07 per hour from 1 July or about 42 cents above the award.

The SDA's Gerard Dwyer said it's a win for workers that Woolworths offered a pay increase matching the 3.75 per cent minimum wage boost, and that legally the supermarket giant only had to offer up the minimum award.

"Absorption was open to them," Mr Dwyer said.

Protest vote

RAFFWU's Mr Callinan said Woolworths and the SDA shouldn't be celebrated for securing a pay boost in line with federal standards, and that it believes workers who fulfil online orders will be left worse off.

"They've used this deliberately misleading language," he said.

In the lead up to the vote, RAFFWU had also been raising concerns about gift cards "inducements" from Woolworths.

Workers were offered a maximum $299 gift card to shop instore with their own employer if they voted yes, along with a second voucher of the same value when the agreement is formally passed by Fair Work.

One Woolworths store worker confidentially described these gift cards as a "bribe" to ABC News, and said they were also concerned that discussion about the EBA was shut down on the workers' internal communication platform, WorkJam.

A few dozen Woolworths workers aligned with RAFFWU stopped work for several hours at the end of last year in protest of the deal, and Mr Callinan claimed those who have raised opposition have been intimidated instore.

"We've had posters torn down. There's been all sorts of nonsense going on," Mr Callinan said.

Solidarity fractured

The division about the deal comes as RAFFWU continues to allege that the SDA is not fighting for a fair deal for its members.

The SDA is one of Australia's biggest unions and is aligned with the union movement's peak body, the Australian Council of Trade Unions, and the Australian Labor Party.

As well as about 70,000 workers at Woolworths, it also has a large membership from the supermarket's rival Coles.

RAFFWU was founded as an alternative union to the SDA.

The Melbourne-based union has long alleged that major retailers help the SDA sign up new members in return for working with them on lacklustre pay deals.

"The SDA has a long-term relationship with Woolworths (which) results in workers being paid such pitifully low wages on pitifully poor conditions," RAFFWU's Mr Callinan said.

The SDA's Mr Dwyer denied these allegations, and also accused RAFFWU of pushing "misinformation" about the pay increase only being in line with Fair Work's boost and for raising concerns about the gift cards.

"A sign-on bonus is not unusual, in fact, its incredibly common," he said.

"There is nothing but good news in this agreement."

In a statement, a spokesperson for Woolworths said the company is "very pleased" that the deal got a majority yes vote and that it will be bringing in the new pay rates from July 1.

By law, if the deal is approved by Fair Work, it will fully come into effect in October.