The lives of about two million train commuters around the country are being put at risk by staff shortages in key positions at the Passenger Rail Agency of SA (Prasa).

The Railway Safety Regulator said yesterday that Prasa's failure to fill vacant positions of train control section managers is mainly to blame for a series of train accidents over the past few months.

It is seeking to ground all trains due to safety concerns.

Train control officers are supposed to have a section manager to verify and supervise all their calls.

The condition was not met when a train rear-ended another in Kempton Park last week, injuring 300 people.

The regulator's spokesperson, Madelein Williams told Sowetan yesterday that it was one of the "special conditions" imposed by them when they issued a one-year safety permit to Prasa last month.

A notice suspending the safety permit was issued following noncompliance with this condition. The suspension has been challenged in court.

"Prasa has failed to appoint section managers to ensure there's countersigning when manual train authorisations were issued and this led to last week's accident," Williams said.

"Due to non-filling of safety-critical positions, they [Prasa] couldn't ensure that they provided a second line of checking during manual train authorisations."

Williams said Prasa had relied on manual authorisations, which were also worryingly growing in number, without supervisors. The authorisations are issued by a train control operator when railway signalling, a system used to direct railway traffic and keep trains clear of each other electronically, is faulty or not functioning due to vandalism, cable theft and ageing infrastructure, among others.

More than 1200 commuters had suffered injuries while 24 lost their lives in five train accidents since January - all happening during manual train authorisations.

Prasa has since approached the North Gauteng High Court in an effort to get an urgent court order that prevents the regulator from suspending the safety permit and grounding all passenger trains.

Prasa spokesperson Nana Zenani said: "In the interest of the ongoing and delicate discussions around manual authorisation as a whole, Prasa reserves the right to comment for now until we have had our key discussions with the RSR."

Meanwhile, transport minister Blade Nzimande has called a meeting for today with the chairs of the RSR and Prasa boards in an effort to avert a high court showdown scheduled for Thursday.

Nzimande's spokesperson Ishmael Mnisi said the minister wanted to ensure that there was an amicable solution reached without having to go to court.

"The minister will not interfere in the RSR's work but he feels they don't need the court because the laws are clear... and both boards can resolve the issues out of court," Mnisi said.

He said the solution has to be in the interest of the commuter without compromising safe and secure train operations.

Mnisi said Nzimande was yet to see the preliminary report on last week's accident in Kempton Park, "so we cannot comment about something that's contained in the reports we do not have yet".

The United National Transport Union, which represents most train drivers, has estimated that more than half of all passenger train authorisations were manually issued.