The Western Australia Local Government Association has told the State Government to keep away from its federal grants.

WALGA made the warning is response to recommendations from the National Commission of Audit, which says the State Government should take control of regional assistance grants and the Roads to Recovery program.

The programs provide important baseline funding to shires and cities across the state, and many would suffer considerably if they were left out.

WALGA’s northern country zone spokesperson Karen Chappel says it feels as though the WA Government will look to distribute the money the way it wants, which may not resonate with the needs of communities.

Ms Chappel said local governments would have to drive up their rates to fill the funding gap if grants were stopped.

“The State Government has shown us that all of a sudden they can have a different priority and if that happened on one occasion, it would decimate our small councils,” she told the ABC.

“Federal assistance grants have been a cornerstone of local government funding for a very long time, they've worked really well.

“They have a methodology that is fair, smaller councils are supported more so than bigger councils and it works, so let's just leave it alone.”

Some have questioned the motive for the comments, as the notion has not been tabled or debated in WA Parliament.