A flag was unfurled on a Princes Freeway overpass in Melbourne's west before dawn on Wednesday morning, and quickly removed by authorities.

There were unconfirmed reports the mysterious flag was emblazoned with the symbol of terrorist group Islamic State.

However, Victoria Police confirmed it was not an IS flag.

"Police were called to a bridge on the Princes Freeway in Laverton just after Point Cook Road, city bound, after reports of a banner on the bridge about 3am," a police spokesman said.

"VicRoads removed the banner. It was not an IS flag and did not contain a threat."

Police are looking into the messaging on the banner, the spokesman said.

VicRoads was contacted for comment but referred questions back to Victoria Police.