This follows the glaring failure of the police to co-operate with the commission.
Mthethwa requested both the commission and Western Cape Premier Helen Zille to suspend its proceedings, but a preliminary sitting went ahead on Monday.
"The rationale behind the setting up of such a commission, which, at a strategic level, only focuses on the South African Police Service (SAPS) and not the Western Cape metro police, is suspicious if not questionable," Mthethwa said on Wednesday.
"Despite the engagements we held with the premier over the past weeks, it is evident that she is determined to continue with the commission by hook or crook, which leaves us with no option but to challenge the matter through the legal framework."
The news of pending legal action came as no surprise to those involved in the commission. Anticipation was high in legal and activist circles that Mthethwa would launch a court challenge to try to bring the commission to a halt before the much-anticipated public hearings begin next week.
The commission on Tuesday issued subpoenas against three local police stations and the provincial commissioner of the Western Cape, Lieutenant General Arno Lamoer, after they failed to respond to requests for information. The requests from the commission were sent to the police on September 6.
The subpoenas were sent to Harare, Lingelethu West and Khayelitsha police stations and Lamoer's office, said Amanda Dissel, secretary to the commission. "We had to subpoena them because we have had no response from the police at all," she said.
The commission had asked the police for numerous documents and records dating back to January 2010, including details of complaints against the police and the criminal prosecution of staff. The commission is investigating police inefficiency and its breakdown in relations with the community and heavyweight commissioners retired Constitutional Court Judge Kate O'Regan and former National Prosecuting Authority director Vusi Pikoli – have been appointed to run proceedings.
Mthethwa asked the commission to suspend its proceedings so the police could do their own investigation of policing problems, but the commission made it clear it would continue with the hearings because it was working to tight deadlines.
Zille launched the commission in August after intense public lobbying by several activist organisations, including the Social Justice Coalition, Equal Education, the Treatment Action Campaign and the Triangle Project. Zille said at the time she had given Mthethwa and the national police commissioner, Riah Phiyega, ample opportunity to respond with their opinions.
There have been more than 18 vigilante killings in Khayelitsha this year and activists have claimed these are directly related to the community's lack of trust in the police to take action against crime.
Cordial and constructive
The M&G has seen a copy of the letter Mthethwa sent to Zille about the commission on October 24, in which he claims to be trying to avoid an intergovernmental dispute.
"I am particularly keen to ensure that the investigation initiated by the national commissioner is finalised as soon as possible," Mthethwa wrote."You will recall that I convened a meeting with you on Tuesday October 9 2012, to discuss my constitutional concerns about your appointment of the above commission. At the end of the meeting, you indicated that you would seek legal advice on my request to you to postpone the commission of inquiry, pending the finalisation of an investigation to be conducted on the instructions of the national commissioner."
Mthethwa emphasised in the letter that he felt his interaction with Zille had been "cordial and constructive".
"I am, with the utmost respect, of the view that your appointment of the above commission may be unconstitutional and irrational, and may breach both the letter and the spirit of co-operative government, as provided for in chapter three of the Constitution and the Intergovernmental Relations Framework Act, 2005 (Act No 13 of 2005)," he wrote: "I have exchanged correspondence and have met with you in order to avoid an intergovernmental dispute. Our interaction has been cordial and constructive. I am, therefore disappointed that you have still not dealt with my request. You have instead posed a number of questions regarding the steps taken by the national commissioner to investigate the matter."
The commission Zille appointed was continuing to do its work. This, Mthethwa said, made it very difficult for him to discuss the police investigation and the concerns Zille might have with the provincial commissioner's plans for an investigation into Khayelitsha policing.
"I have been advised that your commission has addressed correspondence to the state attorney who represents the SAPS, the national commissioner and myself. In that correspondence, the commission has demanded information and has threatened to issue subpoenas to secure the requested information, if necessary.
"I have been informed that the commission has also communicated with other organs of state. This suggests to me that the commission is extending its reach into other areas of the criminal justice system. If this is correct then it would appear that, in effect, you may have exceeded powers which you have in terms of the constitution and that your actions are ultra vires (beyond the powers)."
Mthethwa claimed that the national commissioner might have already completed her investigation into policing in Khayelitsha if the commission had not been appointed.
"The national commissioner did not proceed with that investigation because of your actions in appointing the commission," he wrote.
The work of the commission to date raises Public Finance Management Act issues of possible wasteful and irregular expenditure, Mthethwa suggested. "To resolve that eventuality, I would have no objections to the submissions already made to the commission and the evidence already collected by it being submitted to the investigation panel, when it commences its work."
In response to questions from Zille, Mthethwa provided a plan for the proposed police investigation. The Women's Legal Centre, which is representing several activist organisations, claims the plan is scant in detail and appears to lack the required independence.
Attorney Sanja Bornman from the legal centre told the M&G she had already been instructed to oppose Mthethwa's attempts to suspend the commission and the centre was waiting to view the court papers and consult with the premier.