The council last week said the "dysfunctional" South African Mineral Resources Administration System (SAMRAD) needed to be discarded, as it cited figures from the Department of Mineral Resources and Energy indicating 235 mining rights, 2,485 prospecting rights, 1,644 mining permits, 238 Section 11 change of ownership transfers and 724 licence renewals were currently backlogged.
President Cyril Ramaphosa had last year put forward plans to halve licensing timeframes and DMRE director-general Thabo Mokoena said last week the department was working on the backlog and looking at measures to improve the system.
Over the weekend, the minerals council said it was working closely with the DMRE to get permitting blockages resolved and said it and its members had offered their support to overhaul the system.
The MCSA reiterated its call to discard SAMRAD and develop "a new, transparent and reliable online mining cadastral system".
"A mining cadastre provides extensive information on exploration in the country, allowing investors to track their application," it said.
"In this way it provides investor comfort and prevents mal-administration or corruption.
"Given the importance of a mining cadastral system, the minerals council has offered to contribute towards its reasonable costs, provided the SAMRAD system is discontinued."
It said expedited permitting would "unleash" significant investment.
The country has slid to 60 out of 77 jurisdictions in terms of investment attractiveness in the latest annual Fraser Institute survey of mining companies.
The council named six factors to make South Africa an attractive exploration destination.
These were regulatory certainty, an end to permitting delays and a transparent and efficient prospecting rights application system.
It also listed efficient and cost-effective infrastructure, "properly structured tax incentives" to encourage individuals and entities to invest in exploration, and again called for a flow-through share tax incentive.
Mineral resources and energy minister Gwede Mantashe wants South Africa to attract no less than 3% of global mining exploration expenditure, compared with 1% in 2019.