The Constitutional Court issued a judgment on Thursday clarifying who was responsible for last year's application relating to delays in processing pardons for prisoners.
Last year, it found that the 385 people who had taken the justice ministry to court should have taken the President to court over the matter.
However, it ordered that the costs of the application to itself, and applications to two lower courts, should be carried by the ministry because of delays in the matter.
However, the ministry believed that the order only applied to the Constitutional Court application and payment was not forthcoming, so the court was approached again.
In Thursday's ruling, the court said that although the judgment made it clear that the costs of all three applications should be carried by the ministry, this was not contained in the order it made.
"Although this was clear from the judgment, it was not stated in the order itself. The court therefore varied its order in the previous judgment to remedy the ambiguity," the judges said.
On September 30 last year, Mqabukeni Chonco and 384 others - mostly Inkatha Freedom Party members - successfully sought a court order forcing the President to process their pardon applications, lodged with the justice department as far back as 2003.
In that order, the justice minister and the President came under fire from the court, saying that the long wait was "unacceptable".
In October, nine days after the judgment, the applicants filed their first papers in a follow-up application, saying that the President was now the respondent, and that there had been another delay in processing the pardons.
The President replied to their papers in December, saying that he intended to finalise the pardons by the end of January 2010.
The group, however, decided to proceed with the matter, and a date in the Constitutional Court was set down for February.
When the matter was heard, the President submitted an affidavit with an update stating he had already considered 384 applications and rejected 230.
The costs for that application were borne by the applicants because the court felt they had rushed to them, instead of first trying to establish what the President was doing about the matter.
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