The controversial Biodiversity Conservation Bill has passed through the Upper House of the West Australian Parliament after being amended by the Greens.

The legislation was intended to update the state's conservation laws for the first time in more than 60 years.

It provides for greater protection of habitat and ecological communities and massively increased penalties for killing threatened species.

Members of the public may also make nominations to list a threatened species.

Greens MLC Lynn MacLaren commended Environment Minister Alfred Jacob for acknowledging criticism from the conservation sector.

Ms MacLaren said the so-called 'God clause' was changed so Parliament would now have to debate a minister's decision to allow a species of plant or animal to become extinct.

"There are limits on what the minister can do now thanks to our amendments in the Upper House, we did require that any decision that the minister might make or might want to make about extinctions has to be approved by both houses of Parliament," she said.

Another amendment called on the minister to seek and have regard to scientific advice.

"Our amendments did significantly limit the minister's powers in those two areas that the conservation sector was really concerned about," Ms MacLaren said.

She said she still had concerns about the bill, which was why she actually voted against it despite the acceptance of most of her amendments.

The bill is expected to return to the Lower House next week.