Thursday's move brings to three the number of leaders in the department from the Free State, all newcomers to the mining industry. The others are the minister, Mosebenzi Zwane, and the head of mineral regulation, Seipati Dlamini, who oversees the issuance of mining rights.
The mining industry reacted with dismay to the appointment of Mokoena as director-general. He brings no visible mining experience and little management experience at this level.
Mokoena, the secretary of the Free State legislature, has a law degree from the University of the Western Cape.
He will take up the role in April, filling a position that has been occupied for a year by David Msiza, the chief inspector of mines, after the unexpected resignation of Thibedi Ramontja, who served with three ministers in the department.
The Chamber of Mines said it had been "caught by surprise" by the announcement, over which it had expected to be consulted.
"Consultation with key stakeholders, such as the Chamber of Mines and other relevant stakeholders, is important before [such an] announcement [on the director-general] is made and as the chamber we have been caught by surprise," the industry lobby group said in a statement.
"While the newly appointed director-general is a lawyer by training, there are concerns about the depth of his mining industry knowledge and experience, more so given that the industry has a twin challenge of attracting investments and growing the industry and is also dealing with challenges of transformation and inclusive growth," it said.
Mokoena's CV shows that even his experience in law has been limited. He occupied several junior political positions as a spokesman for the ANC, ANC Youth League and Young Communists League before an unsuccessful stint as the municipal manager of Ngwathe Local Municipality (Parys).
In 2011, while he was still in an acting position at the municipality, ANC secretary-general Gwede Mantashe and the provincial working committee had to step in after a spate of problems. In 2012, Mokoena was made permanent municipal manager, but by 2013 faced allegations of nepotism and corruption. A task team reported in July 2013 that he had offered jobs to his friends and paid them inflated salaries.
It is not clear if any action was taken against Mokoena after the task team's findings, but in 2014 he was appointed secretary of the Free State provincial legislature.
On Thursday, Mokoena referred all queries about his background to the department, which in a brief response said: "Advocate Mokoena has met all the requirements of the post as advertised."
Mokoena said: "It's only today that the Cabinet position was communicated ... and so it would not be professional for me to deal with matters of the department because I am not yet with the department."
He would not immediately comment on the allegations levelled against him when he was a municipal manager.
"I think those are things we can deal with once I have started [at the department]. If you have questions around those issues, I think they will be dealt with at the right time," he said.
Members of the legislature had very little positive to say about Mokoena on Thursday, describing him as "mediocre at best" and "having little regard for cost containment".
The chamber had hoped for strong leadership in the director-general position given the regulatory uncertainty around the third iteration of the Mining Charter and the pending amendments of the Mineral and Petroleum Resources Development Act, which Zwane promised in February would be completed before March and June, respectively.
"Given the significant challenges facing the South African mining sector, including viability issues, policy uncertainty, a [departmental] draft charter that has many unworkable targets, static investment, falling employment and a South African mining industry that is now ranked 74th out of 104 mining jurisdictions in the Fraser Institute ranking for investment attractiveness, all of which will pose significant challenges for the new director-general," it said.
Zwane was plucked from obscurity as the agriculture MEC in the Free State government to be appointed mines minister in September 2013.
Dlamini was chief financial officer in the Free State department of agriculture when Zwane was MEC.
Both were involved in the payment of tens of millions of rand to a dairy project linked to the Gupta family, which went horribly wrong.
Zwane was singled out by former public protector Thuli Madonsela in her State of Capture report for his trip to Switzerland with the Guptas on a mission to persuade Glencore to sell the Optimum colliery to their company, Tegeta Exploration and Resources.
Zwane has denied accompanying the Guptas.
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