The state's department of transport confirmed there was an outage on Thursday afternoon, with most myki fare payment devices at train stations, buses and trams affected.

The outage was rectified shortly after 6.30pm, a department spokesman said.

"Some readers may take time to become operational again but passengers should touch on and off as normal where it is available," the spokesman told AAP.

"We thank everyone for their patience."

It comes after heavy rain lashed the Melbourne CBD on Thursday evening, leaving hundreds of homes without power.

The cause of the outages remain under investigation, according to the Powercor website.

Australian Associated Press