Catharine Kennedy-Lamplough was getting into her car after feeding her horses in a paddock at Mount Cottrell, 40 kilometres west of the city, when she saw a cloud shaped like a funnel twirling in the sky above her just before midday.

"It was like fairy floss dissolving into the bigger cloud," she said.

"The clouds above it were very dark. It was amazing to see."

The 25-year-old hospitality worker quickly pulled out her iPhone and captured the cloud, which she estimated to be near Melton.

And what was running through her mind?

"How quick I could leave the [paddock], basically," she said.

Ms Kennedy-Lamplough wasn't the only person to spot the cloud, with many people posting photos on social media as rain and thunderstorms headed across Melbourne.

The Victorian Storm Chasers Facebook page said it received shots of another one on Monday near Traralgon, in Victoria' east.

But there was nothing to fear, with funnel clouds being mostly harmless.

Bureau of Meteorology senior forecaster Scott Williams said they formed when the temperature fell rapidly high in the sky, as it did in Melbourne on Monday morning.

"They aren't all that common, you normally get about one or two a year," he said.

"Depending on how strong the wind shear is, you can get tornadoes that cause considerable damage, but that's rare around Melbourne."

Mr Williams said once every 10 or 20 years a funnel cloud touched the ground in Melbourne, thus becoming a tornado, causing significant damage.

He said they could rip up trees and damage buildings.

The last one to cause widespread damage was on Christmas Day in 2012, Mr Williams said.