The anti-corruption watchdog body laid the charges on Monday morning.
In a statement the organisation said the charges related to a matter which involved alleged fraud and corruption committed by two senior SARS employees.
In October, Corruption Watch wrote to Moyane over its concerns over the way he had allegedly handled the matter and how he had allegedly breached the Prevention and Combating of Corrupt Activities Act and the Financial Intelligence Centre Act.
The organisation said the breaches stem from Moyane's apparent failures to report the matter to the Hawks.
Moyane has denied any wrongdoing stating that the Hawks had launched an investigation into racketeering and money laundering against the two SARS employees.
Corruption Watch said on Monday it had written to the Financial Intelligence Centre director, Murray Michel, and to the Hawks boss, Lieutenant-General Berning Ntlemeza seeking clarity and confirmation on Monyane's claims, that cases had been opened.
"The financial intelligence centre responded but not the Hawks.
"Corruption Watch is not satisfied with the contradictory statements made by Moyane and the Hawks or by Moyane's explanation in respect of breaches of Fica.
"In the absence of any evidence to confirm averments made by Moyane, the organisation has no option but to proceed with lodging criminal complaints against the commissioner for failing to report these matters to the Hawks."
David Lewis, Corruption Watch's executive director, said: "Arguably the impunity enjoyed by politically well-connected people is the most serious impediment to effectively tackling corruption.
"We are determined that these charges, on the face of it clear violations of our anti-corruption statutes, be investigated and prosecuted. If the Hawks and the National Prosecuting Authority fail in the performance of their duties, we will do in all our power to prosecute these ourselves."
Source: TMG Digital/The Times
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