The rail agency says over 200 train coaches have been set alight this year alone.
Transport Minister Blade Nzimande says Prasa is 'losing money like an ATM' and the RAF board is 'totally dysfunctional'.
Public enterprises minister Pravin Gordhan said the previous board did not take the allegations of corruption at Transnet seriously.
Metrorail says damage to one of its trains, which caught fire between the Bosmont and Maraisburg stations earlier on Tuesday evening, amounts to about R4.5 million.
Former Prasa boss Lucky Montana has denied that his R13.5m property was partly funded with money that can be traced back to a beneficiary of dodgy contracts worth R4bn from Prasa
A subsidiary of TMM Holdings, Siyangena Technologies, scored contentious contracts from Prasa worth R4bn during Montana's tenure as the state-owned entity's CEO.
In court papers, Prasa alleges that a massive security tender was issued absent any tender procedures with the help of some Prasa executives.
"I'm angry because the train doors were open."
Tens of thousands of commuters who use Cape Town's central line are still waiting for Metrorail to say when the train service, suspended since January 8, will be restored.
Prasa has however denied the R1- billion investment is being paid to the bank.