Taxpayers have spent more than $400 million keeping the private companies who run the state’s public transport network afloat and paying for extra cleaning of trains and trams.

The money was forked out as commuters deserted the network during extended lockdowns, with annual patronage on Melbourne’s trains dropping by up to 60 million.

A total of $438 million was spent on public transport during the pandemic, the budget shows.

The government confirmed it paid $75.6 million in total to Metro Trains and Yarra Trams under its relief package, with the bulk of the money representing government losses in farebox revenue.

The remainder was spent on cleaning, a public transport COVID-19 response plan and commercial passenger vehicle services during the pandemic.

An anti-corruption inquiry heard evidence this month that a cleaning company paid millions for extra work during the pandemic failed to properly clean trains on the suburban and regional networks.

The $438 million COVID-19 package adds to the $20 million spent covering the loss in commercial rental revenues for properties owned or operated by the Transport Department, resulting from the government’s rent relief policy for commercial tenants.

Annual spending on transport services blew out the government’s targets this year – by $100 million to $1.2 billion on city train services and $40 million on regional trains, the budget reveals.

While spending on public transport operations soared, commuter numbers plummeted, by 60 million people on the metropolitan train and tram networks and by 6 million on regional services last financial year.

However, the government forecasts that commuter numbers will return to pre-pandemic levels next year.

Key rail programs received funding in this year’s budget, including the $2.2 billion Suburban Rail Loop and $2 billion for Geelong Fast Rail.

However, none of the $2 billion for the Geelong upgrade has been allocated over the forward estimates, pending negotiations with the federal government, while $420 million was set aside for the Suburban Rail Loop this financial year. More than $1 billion was allocated over the next two years.

This adds to about $1.5 billion allocated to 100 next-generation trams to be manufactured at a new facility in Melbourne’s north-west, creating 1900 jobs. This will see a new claass of tram rolled out by 2025 to phase out the ageing A- and Z-class fleets.