South African National Roads Agency Limited (Sanral) CEO Nazir Alli's salary package did not increase by R1.1-million but by R332 000, the company said on Tuesday.

"It is also important for the sake of fairness that the context in which salary increases occur, are stated," spokesman Vusi Mona said in a statement.

"The CEO's salary is determined by Sanral's board and approved by the minister of transport."

Mona said Alli's annual salary of R1.56-million was adjusted to R1.89-million according to the annual report.

On Saturday, Beeld reported that Alli's salary package had increased by R1.1-million compared to the previous financial year.

According to the report, Alli presently received a total package of R3.06-million and a bonus payment of R679 000, while his total package in 2012 was R1.91-million excluding bonuses, according to Sanral's yearly statements published this week.

To say he received a bonus this year and not last year and simply add that to his salary was at best an indication of basic misunderstanding, Mona said.

A bonus was not and had never been part of a salary, he said. The reports over the weekend were wrong.

"The reports are simply mischievous, or worse, prejudice is colouring views."

He said South Africans should be having a rational discussion about the state of the roads.

There was no argument about the quality of the national roads, the high-level engineering and the "solid administration and Sanral's clean financial bill of health".

"Clearly misleading reports about the CEO's salary detracts from these achievements while adding nothing to the rational debate around our roads. That is deplorable," Mona said.

Sanral received an unqualified audit. However the auditor general warned that the company's situation needed to be watched.

Sanral's balance sheet indicated it had an accumulated loss of R4.7-billion, Beeld reported.