The Greens have lodged a formal complaint with Labour over outspoken MP Shane Jones' attacks on the party.

It comes as the Northland-based list MP faced a ticking off from leader David Cunliffe this morning over his anti-Green comments as well as for straying into other MPs' areas of responsibility.

It is understood the Green's chief of staff Ken Spagnolo invoked the official mechanism for airing disputes with Labour's new chief of staff Matt McCarten and it will be on the agenda of the next top level meeting between the two allies.

Green co-leader Russel Norman said he imagined the matter would be dealt with at chief of staff level.

But he said Labour was obviously had some "internal issues" to deal with.

''There's clearly some people like Shane Jones within Labour who are uncomfortable about protecting the environment and embracing our clean energy future. but ... the Greens know what we are doing and why we're here."

Meanwhile Cunliffe confirmed he had spoken to Jones about straying outside his portfolio areas and using strong language to attack the Green Party.

But he had not been disciplined

"I've spoken to him. The message to caucus is ...that all of us are consulting with our colleagues if we are crossing portfolio and manage our comments in a proper way."

He said Jones was a much-valued colleague but occasionally his rhetoric crossed the line. There was a clear understanding not to attack potential coalition partners.

At the weekend Jones criticised the number of foreign university students - a responsibility that crossed the roles of Grant Robertson and Raymond Huo. Cunliffe said it was a heat of the moment debate comment and fully understandable.

Jones, who has been vocal in his attacks on the Greens and is seen as preferring a deal with NZ First, yesterday called Green oceans spokesman Gareth Hughes a "mollyhawk" for opposing offshore iron ore extraction.

Jones said Hughes was undermining the Environmental Protection Agency by commenting ahead of a hearing to consider an application by Trans-Tasman Resources to mine iron ore from the seabed off the west coast of the North Island.

The Greens' activist stance was inappropriate for a government-in-waiting, Jones said.

But Hughes said the mollyhawk reference was "funny" and 'just Shane'.

If Jones had done his homework he would have known that his own Labour colleagues had made similar comments about the Tukituki dam and the Kapiti Expressway, Hughes said.

Heading into Labour's caucus meeting today, Cunliffe said Jones was not reflecting his position on the Greens.

"I would have chosen different words."

Jones was the economic development spokesman so had a legitimate interest in mining, he said.

"We have a strong and deep relationship with the Greens as we do with other potential coalition partners."

Cunliffe said he would work with whatever cards the voters delivered after the September 20 election.

"That may indeed quite likely be with the Greens, it may well be with Winston first ... NZ First," Cunliffe said.

"They are both wonderful parties."

He would not say the Greens would be his first choice, saying there was "no preordained order".

However, his first call after the election would probably be "to the next biggest Left of centre party".

NZ First was centrist, he said.

Prime Minister John Key said it showed tension within the Labour caucus.

"We've been saying for quite some time there are divisions within the Labour Party and they're probably just bubbling up the surface."