Maswanganyi said there were private companies at Prasa investigating the matter and his department was equally concerned with the irregular expenditure which had not been budgeted for.
He said following recommendations by the public protector, the National Treasury was more than equipped and had the competency to investigate.
“The Treasury should have been left to do its work unhindered and we are to make sure it is done efficiently and ensure we don’t incur unnecessary expenditure by paying private companies.”
“There is no cover-up and no minister has interfered with the ongoing investigations. Whatever the courts decide we will abide by,” he said.
The minister added that his department would also establish a strong institutional capacity to complement the basic investigative work conducted by institutions to combat all elements of criminality within the transport SOEs.
The over-expenditure at Prasa is being looked into by the National Prosecuting Authority (NPA), the Special Investigating Unit (SIU), the Public Service Commission (PSC), the Financial Intelligence Centre and the auditor-general following the public protector's report titled: Derailed which revealed that corruption within the institution had cost it millions.
Maswanganyi was briefing the media in Pretoria regarding the performance of SOEs for the 2015/16 financial year.
Prasa was said to have only partially met 10% of its predetermined objectives during the 2015/16 financial year, achieving 45% compared to the 35% in the previous year.
The SA National Road Agency (Sanral) received an unqualified audit report from the AG and attained 99% of its performance target for the 13th year in succession.
The Road Accident Fund (RAF) obtained 90% of its APP targets and managed to reduce the number of outstanding claims to 217182 by March 31 despite an increase in unregistered claims.
The minister said the Road Traffic Infringement Agency (Rtia) improved by 81.3% despite operational challenges.
Through intensified road safety and law-enforcement programmes and marketing campaign efforts the Road Traffic Management Corporation’s (RTMC) had achieved 92%.
South African Civil Aviation Authority, Airports Company South Africa, and the Rail Safety Regulator also came in with high performances, well above the 90% mark.
Additionally, the South African Maritime Safety Authority, Air traffic and Navigation Services and Cross-Border Road Transport Agency came in over the 65% mark for their performance.
Maswanganyi said all SOEs would be expected to submit turnaround strategies to ensure accountability to the electorate and good corporate governance.