Fuelling the current disquiet was the decision to first renege and then honour a written agreement with the Palmer United Party for an inquiry into the Queensland government's environmental record, among other things.

There are also concerns within the Greens' party room that the decision to bluntly oppose the Abbott government's proposed reintroduction of twice-yearly fuel excise indexation is inconsistent with the Greens' general ethos of lifting cost penalties on fossil fuel consumption.

A Greens source said the fuel tax issue had not been adequately debated, despite a view by some senators that the party should have offered the government a deal to back the indexation – securing $4.1 billion over four years – in exchange for protection of the renewable energy target.

With the RET subject to a withering assessment by conservative critics, one Greens insider described that possibility, were it able to be achieved, as "a win on both counts" for the environment.

The Senate inquiry into Queensland was finally established on September 30 and will report back by March 27, 2015, under the chairmanship of PUP senator Glenn Lazarus.

But it only came about after first being scotched in the Senate a week earlier.

Correspondence obtained by Fairfax Media between Greens Queensland senator Larissa Waters and PUP senator Zhenya "Dio" Wang shows the two parties had settled on terms to establish an inquiry into the performance of Campbell Newman's government, which green groups say has ridden roughshod over environmental concerns in favour of major coal and other development projects.

In a letter to Senator Waters dated September 22, Senator Wang advised the PUP would vote against the Abbott government's proposed Environment Protection and Biodiversity Conservation Amendment (Bilateral Agreement Implementation)Bill 2014, "and any future bill which facilitates giving away federal environmental approval powers".

That had been a key stipulation of the Greens, who had made support for an inquiry into the record of the Newman Liberal National Party government conditional on PUP voting against the amendment bill in the Senate.

In a return letter the following day, Senator Waters wrote: "The Australian Greens will support the revised Palmer United Party motion to establish an inquiry into certain aspects of Queensland government administration related to Commonwealth government affairs."

However, when the Greens backed a Coalition amendment to include the Bligh Labor government in its purview – a move that automatically denied the inquiry the support of either of the major parties – the attempt to establish the inquiry collapsed.

Some environmental groups that are normally regarded as central to the Greens' constituency were upset and applied external pressure on the leadership, forcing it to reverse its position.

Groups representing the solar and alternative energy sector, and rural interests such as those opposed to coal seam gas, called on the party to change its mind to back the inquiry.

The two issues remain points of tension in the conservation sector and risk becoming focal points for criticism of Christine Milne's leadership.

Senator Waters said the second version of the inquiry terms had been improved to include specific reference to coal seam gas regulations in Queensland.

"We have successfully negotiated the best possible outcome for the environment," she said.

"We secured improvements to the terms of reference which have enabled investigation into both the environmental attacks of the Newman government and the dodgy coal seam gas approvals of the Bligh government.

"The Greens have ensured this inquiry is even-handed through our improvement to the terms of reference that ensured the Bligh government's CSG approvals would be investigated.

"Through our negotiations with the Palmer United Party, we have secured an agreement to block Tony Abbott's plan to hand federal approval powers over to state governments."

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