The Environment Centre NT (ECNT) announced last month they were taking Resources and Water Minister Keith Pitt to court, challenging the lawfulness of a $50m grants scheme which was used to award $21m to Empire Energy for the purpose of gas exploration in the Basin.

In a federal court hearing in Sydney on Tuesday, Justice John Griffiths said the Australian Government Solicitor, acting on Mr Pitt's behalf, had assured the court via a letter on September 3 that the grant would not be finalised for "two or three weeks."

However, Justice Griffiths told the court the grant was finalised six days later, without telling the ECNT.

Barrister for the ECNT, Oliver Jones, said his client found out the grant had been finalised via an announcement by Empire Energy on the Australian Stock Exchange (ASX).

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"There has been behaviour here that is unfair and misleading," he said.

"There may be some explanation, but none has been put before the court today."

Justice Griffiths ordered Mr Pitt's legal team to provide an affidavit explaining why the grant was finalised before the proposed time without informing the other party.

"Why the sudden haste, Miss Caristo?" Justice Griffiths asked lawyer for the AGS Megan Caristo.

"Why was the applicant not told there had been a change in direction?"

He said the events could "only be described as unfortunate" and "not reflecting well on the minister."

Ms Caristo apologised on behalf of her client, saying the lawyers for the AGS were "doing the very best they can."

Mr Jones requested that a hearing into the matter be expedited "in light of what's happened", with the hearing listed to take place on November 2 and 3.

Justice Griffiths ordered the AGS pay costs to the ECNT for the case management hearing.

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