The proposed $2 billion passenger railway servicing Perth Airport has been recommended for approval by the Environmental Protection Authority (EPA).

The eight-kilometre railway is proposed to branch off the Midland line in Bayswater and pass through twin tunnels under the Swan River and airport runways.

Three new stations will be built, one at the domestic terminal, one at the international terminal and another in Forrestfield.

EPA chairman Paul Vogel said the most significant environmental impacts would be at the site of the proposed Forrestfield station.

"There's a significant threat there, although it's only clearing 1.6 hectares of that threatened ecological community," he said.

"There are 25 plants of a very rare flora species.

"They need to be very careful about how that manage direct and indirect impacts.

"There were no significant impacts on animals that would require assessment and conditioning by the EPA."

Dr Vogel said the Public Transport Authority believed there was no way the project could avoid impacting on the ecosystem.

He said tunnelling under the Swan River would produce nearly 750,000 cubic metres of spoil.

"We think there are tremendous opportunities to re-use that material, so rather than just dumping it in the landfill, let's see if we can make productive re-use of that," Dr Vogel said.

"There will need to be dewatering and they may encounter acid-sulphate soils."

Environmental offsets recommended

Dr Vogel said the EPA recommended Environment Minister Albert Jacob approve the project on the condition that a number of environmental offsets were adhered to.

"The Public Transport Authority will need to come up with an adequate offset strategy within 12 months of approval," he said.

"That has yet to be determined, but they will have to come up with something that satisfies the Government offsets policy."

He said the PTA would also need to produce a flora and vegetation monitoring and management plan.

"They will need to ensure and provide confidence to the community and to the Government that those impacts are manageable," Dr Vogel said.

The EPA said federal legislation required a separate environmental assessment to be completed for the section of rail that passes through the Commonwealth Government-owned Perth Airport site.

The EPA's report is now subject to a two-week public appeal period, before the Minister makes a final decision on the project.

There have been calls for the entire rail project to be scrapped as WA debt skyrockets and the number of fly-in fly-out workers falls.