He said the NPA Act requires every member of the authority to act without fear, favour or prejudice.
"Instead they have acted with fear, favour and prejudice to advance some or another political agenda, further eroding the little trust South Africans might still have left in them," he wrote on Thursday night.
"It is, indeed, shameful."
Two weeks ago, 34 striking workers were shot dead by police who were trying to disperse them at the Lonmin Mine in Marikana.
Another 78 were injured.
Initially, the arrested group was charged with public violence. On Thursday, the NPA announced they would also face murder and attempted murder charges for the death of their colleagues.
De Vos said the decision represented "a flagrant abuse" of the criminal justice system.
"Unless what we saw on our TV screens never happened or unless the NPA is hiding shocking and bizarre conspiracy theory-type evidence from us.... there could be no possible valid reason for the NPA to have charged the miners with murder..." he said.
He said even if the miners provoked the police, this could never make them liable for the killings.
"Perhaps they [the NPA] are clumsily trying to stigmatise the miners in the eyes of the public....Maybe they are trying to intimidate the miners in an attempt to break their spirit."
The Congress of SA Trade Unions (Cosatu) said it was outraged by the decision.
Spokesperson Patrick Craven said it exposed the lack of proper training within the SA Police Service and the NPA for failing to find evidence and charge those responsible for the offence.
'Their own version of the facts'
"The NPA should have waited for the findings of the judicial commission of inquiry, which is tasked with uncovering the truth...before jumping the gun and laying such charges," he said in a statement on Friday.
"It is showing its contempt for the inquiry and potentially jeopardising its independence and relevance by pre-judging the arrested workers on the basis of their own version of the facts."
In an open letter to President Jacob Zuma, the United Democratic Movement (UDM) called for an intervention in the matter..
"The police have blocked every attempt by the mineworkers to get bail because they claim that they are still busy with investigations," the party's president Bantu Holomisa said.
"Yet, the NPA has already taken a decision to prosecute the mineworkers even though the investigation is incomplete."
It appeared as though other arms of government already knew who was to blame for the shooting, said Holomisa.
He said this undermined the role of the commission of inquiry.
"We call on you [Zuma] to halt the unfair prosecution of mineworkers and to urge everyone to allow the... inquiry get to the bottom of the Marikana massacre."