The list of mines was supplied to the Mail & Guardian by the department's director for communication services, Mava Scott.
It includes at least five mines owned by Cyril Ramaphosa's Shanduka Group, as well as operations falling under Anglo Platinum and Harmony Gold.
Two operations have not yet applied for licences, including Gold Fields' Beatrix mine.
Gold Fields's corporate affairs manager, Sven Lunsche, said that Beatrix could still operate legally because prior legislation "made provisions for previous permits … Nevertheless [they] are currently in the process of applying for a licence … [and they] expect the application to be in during the next two months."
The department's documents show that Vunene Colliery in Gauteng has also failed to apply for a water licence, although its status is given as "pre-application". Vunene had not responded to the M&G's queries by the time of going to print.
Harmony Gold's Doornkop mine in Randfontein, Gauteng, is also non-compliant, although its application is shown as being "in process". Harmony spokesperson Marian van der Walt said the operation was legally compliant in terms of the 1954 Water Act. However, the company had applied to the department to convert old-order to new-order rights.
It was liaising with the department to expedite the issuing of the licence, said Van der Walt.
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The documents show that PMG Mine, a manganese mine in the Northern Cape, must submit additional documentation to the department to finalise the licensing process.
PMG chief executive Shirin Ismail said the company had contacted the department "to remedy the situation". A meeting between the parties would take place this week.
One of Anglo Platinum's operations in North West is also listed as non-compliant. The company had not responded to questions at the time of printing.
The chairperson of Parliament's water committee, Johnny de Lange, said companies' failure to apply for water licences amounted to lawlessness.
"We have created a situation of anarchy. Water can be used only with a licence. We have told the department that it must act. It must stop operations in all companies that do not have licences," he said. De Lange would not comment on individual companies.
"It is unfair to all of us if some companies are allowed to operate without a licence. I don't care who the person is. Every company needs to rectify the situation."
Water use a particularly sensitive issue
Water licensing is not a legal technicality. It is designed to ensure that water is properly managed in a semi-arid country to protect against water pollution, including acid mine drainage, oversee the equitable distribution of a life-sustaining resource and ensure that industrial users pay for consumption.
Because it is a heavy consumer and can inflict major damage on the environment, there is particular sensitivity over the use of water in the mining industry.
The licensing process is set out in the National Water Act, which stipulates that all companies granted mining permits must apply to the water affairs department for a water licence in order to operate legally.
After registering with the department, companies are required to fill out forms specifying their water usage for operational purposes. Failure to register is a prosecutable offence and mines must comply with the guidelines spelled out in their licensing contract with the department.
Before mines are granted a water licence, they must submit to a comprehensive environmental monitoring and assessment programme that looks at what the impact their activities are likely to have on the water system.
The department has strict guidelines on water pollution and each mine has the added responsibility of ensuring that it reports instances of pollution to regional departmental heads.
In a measure designed to avert water shortages, all mines are allocated a predetermined amount of water for use annually and it is their responsibility to ensure that this is not exceeded.