The Department of Environment and Climate Change has twice urged mine owner Xstrata to give serious consideration to avoid mining areas at a low depth under streams, but the company has refused.

The Department of Planning, which is assessing Xstrata's plan, will have the final say on the matter.

The environment department said the low-depth areas were almost entirely in the government-owned conservation reserve.

The environment department has raised its concerns in a submission to the planning department.

The environment department said the plan could cause subsidence leading to loss of water flow and vegetation, threatening wildlife and ecosystems.

In a report to the planning department, Xstrata said cracking was only possible in an 84-hectare area, less than 11 per cent of the mining area.

The environment department said Xstrata planned to monitor changes and wait for any cracks to close naturally before taking remedial action.

Xstrata said regular checking and resealing of cracks would occur, but its report makes several references to the ability of cracks to "self-heal" with fine soil filling cracks.

The Xstrata report said remediation would probably be limited to areas where there was a potential public risk.

The report said if remediation was required small bulldozers would remove the canopy, shrubs and ground layers to gain access.

The environment department said crack repairs had "mixed success in recent years in NSW and often required significant vegetation clearance and vehicle access".

Xstrata says its plan, which includes mining up to 5.5 million tonnes of coal a year over the next 10 to 12 years, could cause up to 2.5 metres of mine subsidence.