Hundreds of metres of railway track laid just two years ago as part of the most expensive public transport project in Victoria's history will be ripped up and replaced over the weekend because it is damaged and has damaged the wheels of V/Line trains.

The track replacement work will require the shutdown of part of the $3.65 billion Regional Rail Link, which has been in full service for less than seven months.

Eight hundred metres of rail on the tightly curved flyover between North Melbourne and Southern Cross stations will be replaced this weekend.

The root cause of the wheel damage is still being investigated by Monash University rail experts, who are due to report on the issue in March, but the decision to replace the tracks on the rail flyover effectively confirms it is one of the chief causes of accelerated wheel wear on V/Line’s VLocity trains.

The wheel wear and an unrelated boom gate failure in Dandenong last month have crippled V/Line rail services for weeks and cost the state tens of millions of dollars.

At the peak of the crisis as many as 70 services a day were cancelled and replaced by coach, prompting former V/Line chief Theo Taifalos to resign under intense pressure from the Andrews government.

Damaged track on the Geelong and Ballarat lines are also set to be replaced.