Vienna's MA 58 water authority said that it would be charging the operator of the course with “failing to manage his facility properly” and a failure to ensure adequate safety conditions.
A spokeswoman told Austrian media that since Sunday's accident people have come forward with stories of previous accidents involving the cable system which went unreported.
The course - which reopened on Monday - has now been closed “to avoid endangering people further”.
An unannounced check of the course by authorities on Tuesday uncovered "numerous irregularities”.
They found that too many wakeboarders were using the cable system at one time and that the officially prescribed safety distance between each person was not complied with.
They also noted that the entire course is not visible from the starting ramp - which means that other boarders and the operators would not spot an accident as soon as it happened.
The inspectors saw several crashes and noted that one boarder was not wearing a safety helmet. Staff who were employed at the course did not have a license to operate a lifeboat for emergencies.
A similar accident, where someone got caught in the cable, had happened ten days before the woman lost her arm, but was never reported.
The operator of the course, Michael Machek, said in a press release on Monday that the course had been “tested dozens of times, with no complaints”.
It's still unclear how exactly the 41-year-old woman from Vienna lost her arm. Police said they hoped to question her on Thursday.