However, Mboweni said on Thursday he was was not happy with Sanral's decision, saying it undermined what the Treasury had said in its budget - that it supported the "user must pay" principle.
Mboweni made the comments during the introduction of the new South African Revenue Service (Sars) commission, Edward Kieswetter, in Pretoria.
"They must reverse that decision immediately or else this has implications for the bond market. It has implications for the fiscus. It has implications for their own credit rating and the credit rating for the country," Mboweni said.
Mboweni said people should ensure they did not take careless decisions in the middle of a very difficult financial situation.
"So pay your taxes, render unto Caesar what belongs to Caesar," Mboweni said, quoting Jesus in the Bible.