The 13th edition of the report shows whites constituted 72.6 percent of top management positions in the country last year, down from 81.5 percent in 2002.
The report reflects the public and private sectors.
Blacks occupied 12.3 percent of top management positions in 2012, compared to 10 percent in 2002.
Commission chairman Dr Loyiso Mzisi Mbabane handed the report to Labour Minister Mildred Oliphant during a Transformation Indaba in Boksburg, on the East Rand.
Coloureds occupied 4.6 percent of top management positions in 2012, compared to 3.4 percent in 2002; and In Indians 7.3 percent, from five percent.
The number of foreigners in top management positions in 2012 was 3.1 percent, compared to zero in 2002.
However, this was because the labour department started collecting this data only in 2006.
Mbabane expressed disappointment at the levels of transformation.
"It is unacceptable. This is not what you would expect, especially because we have a law," he said.
"If we did not have a law like the Employment Equity Act of 1998, you could say people are trying their luck and they are not understanding it, but you have a law that says specifically you must have a [employment equity] plan.".
The government had expected companies to be planning to have put into effect their employment equity plans by 2000.
"The two percent increase in black people occupying top management positions says that either we don't take those [employment equity] plans seriously, or we never took the act seriously. It is not acceptable," said Mbabane.
The report was compiled by the Employment Equity Commission using millions of employment equity reports from the public sector and private companies across all sectors of the South African economy.