Public Transport Victoria's chief has apologised to commuters for Monday morning's train meltdown saying the authority had failed in its job after lightning and flooding knocked out the system.

PTV's chief executive officer Mark Wild apologised to commuters who endured hours of train stoppages, line suspensions and slower services.

"First thing I would say is I am obviously very, very sorry for the inconvenience to our customers today, particularly on such a bad weather morning," Mr Wild told ABC Melbourne.

"It is our job to get people in on the morning and we are clearly not doing a good job of that," he said.

At least five lines were suspended, including Glen Waverley, Upfield, Sandringham, Cranbourne and Pakenham and only two train lines were travelling through the City Loop for about 45 minutes from 6.45am. It took Geelong commuters about an extra hour longer than usual to get to Melbourne.

Some commuters took so long to make it to their destination they were charged for an all day fare on their myki card rather than a two-hour fare.

Mr Wild said Metro Trains was concentrating on getting the afternoon service on track, after lightning strikes and power surges caused up to 60-minute delays and suspended lines this morning.

Metro Trains spokeswoman Larisa Tait said "good services" returned by noon with services operating on time or up to five minutes late.

The only fault remaining was on the South Morang line at Regent station where a team was working on fixing the fault, but this was not affecting services, she said.

At its height, Flinders Street suffered a power surge that cut the number of platforms that trains could use by half. One of the Melbourne's busiest tracks was brought to a virtual standstill, between Caulfield and Richmond, when trains were delayed by an hour on the Cranbourne, Pakenham and Frankston lines.

Mr Wild blamed the "exceptional storm" and the ageing signalling system for the train meltdown. He said lightning strikes, vehicle accidents and other traffic light issues had affected the system.

Drivers hoping to avoid the train strife fared little better in the morning with inbound Monash Freeway traffic taking 100 minutes to complete a journey that can take as little as 30 minutes.

The evening peak is not forecast to be much better. With the wet weather and train disruption sending drivers to their cars in the morning, more cars would be on the road and long delays could be expected, VicRoads acting director of road operations Damien Afxentis said. He said the roads may be slippery and some traffic lights may not be working.

"Following the storms overnight and this morning, there remains a number of traffic lights not operating across the network so please approach these intersections with caution," Mr Afxentis said.

He reminded drivers who approached traffic lights with faults to remember to give way to the right or follow emergency service officers' directions.

Earlier, about 30 traffic lights were out in the CBD.

"We ask all drivers to please drive to the conditions, slow down in heavy rain, remain patient, keep a safe braking distance, turn on your lights and allow extra time for your journey," Mr Afxentis said.

Melbourne Airport experienced long delays after the tarmac was evacuated several times.

Qantas reported that it would continue to try to "catch up" with delayed flights with delays of half an hour still reported by the afternoon. A spokeswoman said passengers should check with the carrier for updates.

Virgin Australia reported it had delays of up to 45 minutes but it was "back to normal" by 2pm.

If you see any road hazards please contact 13 11 70 and check victraffic.com.au for traffic updates.

- with Robyn Grace