A $1 million cash splash by the National Tertiary Education Union to help struggling federal Greens MPs to hold their seats in September has split both the party and the union and led to claims of favouritism as fissures threaten to muddy the deal before a dollar has even been spent.

The tie-up was brokered this week at a fiery meeting of the NTEU’s 120-member national council in Canberra against the backdrop of a meeting of minds over Labor’s $2.3 billion in cuts to the sector to help pay for its Gonski reforms.

But NTEU NSW divisional secretary Genevieve Kelly told Crikey 40% of council had voted against the decision.

“It wouldn’t be any surprise that there was vigorous debate about the amount and where to spend it,” Kelly said, adding that decisions of the council were binding and that she was not at liberty to dispute them after the fact. “There were three days of a hot debate, some people were for and some people against.”

She says the union has specifically ruled out giving any money to the Greens for expensive television advertising and that all campaign material will be produced under a union banner.

Crikey understands delegates from Queensland and NSW were opposed — specific assistance for Western Australia Greens Senator Scott Ludlam and South Australian Senator Sarah Hanson-Young to maintain the current balance of power in the upper house drew opprobrium, as did support for Andrew Wilkie in the Tasmanian seat of Denison, with prominent Greens arguing their candidate Anna Reynolds should be festooned with largesse instead.

A number of senior NTEU officials are also Greens members. The party’s premier Victorian numbers man Ken McAlpine is an NTEU national education and training officer and his partner Linda Gale is a senior NTEU industrial officer. Victorian NTEU secretary Colin Long ran for the Greens at the 2010 Victorian state election in the upper house seat of South East Metropolitan. And NTEU national secretary Grahame McCulloch served on the Greens’ national campaign committee. All are believed to have been open about their conflict of interest.

Annoyed senior NSW Greens sources say they expected most of the resourcing to be limited to South Australia and Western Australia, as well as Adam Bandt’s bid to hold the marginal lower house seat of Melbourne. The money is meant to be targeted in seats where the Coalition is not competitive, but Cate Faehrmann’s bid to beat off the Coalition or Pauline Hanson in NSW, Adam Stone’s Queensland Senate tilt and Simon Sheikh’s ACT campaign have all escaped the NTEU’s Midas touch.

Crikey first revealed the looming donation two weeks ago, when Greens national campaign director Chris Harris said it was possible the NTEU would “support” the party. However, after the story was published Harris rang back to claim he was misquoted and had never mentioned anything about money. Queried as to how the union could support the party without money, Harris claimed that because it and the Greens had a similar position on higher education policy, the union supported the party by default. He then emailed through a list of internet links showing how their positions on higher education lined up.

NTEU president Jeannie Rea issued a statement on Tuesday saying the union’s rationale was to “use the balance of power to block any further university cuts and any future Coalition industrial relations measures aimed at undermining trade union and collective ­bargaining rights”.

A significant proportion of the cash will go to Bandt in his battle to hold his federal seat of Melbourne against Labor challenger Cath Bowtell — Bowtell started as an organiser at the NTEU in 1988 before ascending to assistant state secretary.

Bowtell told Crikey that while it wasn’t for the Labor Party to tell unions how to campaign, she had “a really long track record advocating for tertiary education, VET schools and early childhood education and no one asked what my view was, which was disappointing”.

“Labor actually rebuilt tertiary education funding after the declines under conservative governments — even the Greens acknowledge that. If I was still at the union I wouldn’t necessarily be giving money to a minor party. The union has steered clear of partisan politics in the past so I’m surprised they’ve taken such an overly partisan approach this time,” she said.