Molewa submitted the suggested amendments for public comment on September 30. These covered the norms and standards for marking rhino horn and trophy hunting of white rhino, the department said in a statement on Friday.
"The proposed amendments are intended to address the abuse of the permit system," said spokesperson Albi Modise.
"Although illegal hunting is the main threat that could impact on the survival of rhinoceros in the wild in the near future; stricter provisions relating to hunting [are] required."
This was to ensure that the processes were standardised and to reduce possible abuse of the system.
"The department... views this in a very serious light and is committed to the fight against rhino poaching and abuse of the permit system," said Modise.
The amendments stipulate that all live rhino sold and transported must be micro-chipped in both horns.
Rhino horns obtained as a result of dehorning, which were not micro-chipped, will now have to be micro-chipped by the permit issuing authority.
The information would then be kept on a provincial and a national database.
It was also proposed that all rhino hunts be strictly controlled.
This would be by means of an individual threatened or protected species (Tops) hunting permit which would ensure that all horns could be traced to where the hunt took place.
The hunting of rhino may, therefore, not be authorised in terms of a standing permit for game farms, or a game farm hunting permit provided by the owner of a registered game farm.
The amendment proposes that a person may only hunt and export one rhino for trophy purposes within a 12-month period.
The hunting could also take place only under the supervision of a conservation official, preferably an environmental management inspector (EMI) from the province concerned.
The supervisor must then immediately hand over the information and microchip numbers to the department.
Any exports of rhino horn must be endorsed by the EMI, the department said.
DNA samples would have to be collected when rhinos were darted for translocation and treatment.
Samples would also have to be collected from detached horns obtained through, among others, natural mortalities and dehorning.
"The results of these DNA samples aim to assist enforcement officials to achieve successful prosecutions during criminal proceedings," said the department.
The samples would then be sent to the Onderstepoort Veterinary Genetics Laboratory as soon as possible.
Anyone who wanted to submit representations or comments on the proposed amendments could do so during October.
It is estimated that 307 rhino have been poached so far this year. In 2010, 333 rhino were poached.
About 180 people have been arrested this year, up from 165 last year.