The Queensland Government has launched legal action against the owner of a Cape York cattle station at the centre of a land-clearing controversy for allegedly breaching an obligation to care for Indigenous heritage.

The owner of Kingvale Station on the Cape York Peninsula legally cleared 500 hectares of land before the Federal Government intervened in 2016, over internal concerns about the effect on sediment run-off into the Great Barrier Reef.

The traditional owners of the land, the Olkola people, claim the owner of Kingvale Station went ahead with the clearing without their knowledge and may have destroyed a burial site.

The ABC can reveal the Queensland Department of Environment and Science is taking court action as a result of an investigation which started as early as 2016, when the Olkola people complained to the Government that they believed Kingvale Station may be in breach of the Aboriginal Cultural Heritage Act.

In a statement, a spokesman for the Department of Aboriginal and Torres Strait Islander partnerships said the court action was lodged last week.

"The alleged contravention relates to one offence against section 23(1) of the Aboriginal Cultural Heritage Act 2003, for carrying out an activity and failing to take all reasonable and practicable measures to ensure the activity did not harm Aboriginal Cultural Heritage," the spokesman said.

"This matter is due to be considered in the Cooktown Magistrates Court on 5 July 2018."

The Queensland Government would not detail the exact detail of the allegations before the court.

Lawyer Dave Kempton, who acts for Kingvale Station owner Scott Harris, declined to speak to the ABC due to the legal action other than to deny the Olkola people's allegations.

'Things can happen without you knowing about them'

Olkola Aboriginal Corporation chairman Mike Ross said he wanted to be consulted further about the clearing.

"If they're doing broad-scale clearing, any sort of activities on your country, first of all we should have a look at it, get together and at least talk about it, you know?" he said.

"It's very remote in this area here. Things can happen without you knowing about them.

"If development happens on anybody's tribal area it should be negotiated from day one."

The land clearing was initially approved by the former LNP Queensland Government headed by Campbell Newman.

Mr Ross said he and his brother did an aerial survey over part of Kingvale Station under the previous owners to survey burial sites located years earlier.

The action comes as the Federal Government considers its final decision on the next stage of clearing at Kingvale, which would remove 1,800 hectares of tree cover for grazing.

That decision has come under fire from environmental groups, who claim the Government is undermining its recent $500 million commitment to protect the Great Barrier Reef by approving the clearing.

A Federal Environment Department spokesman said the court action would not delay their decision on that matter.