Presidency spokesperson Mac Maharaj said Godongwana had resigned to "pursue personal interests".
President Jacob Zuma had accepted the resignation and thanked the deputy minister for his dedicated service and duty to his portfolio and to the national executive in general, he said.
In June, Godongwana and his wife, Thandiwe, were reportedly linked to a company that disappeared with R100m in workers' pensions.
The SA Clothing and Textile Workers' Union (Sactwu) is trying to get back the R100m of pension funds from an investment company.
Deal
It was reported at the time that the money had been placed with Trilinear Empowerment Trust, which in 2007 agreed to lend R93m to Canyon Springs Investments 12 to buy an unnamed and unlisted company.
The deal did not happen.
Canyon Springs Investments 12 could not repay the loan as it had allegedly "lost" the workers' money.
The Godongwanas acknowledged to The Star newspaper that one or the other of them had been linked to Canyon Springs since at least November 2007.
They said Enoch Godongwana had been chairperson from November 2007 to May 2009, while his wife had been a non-executive director since May 2009.
The loan payments were made from March 2007 to December 2009, and the loan agreement was signed in February 2009.
The Cape Times reported on Monday that, according to Maharaj, Godongwana had approached Zuma in December asking to be relieved of his portfolio, but the president had asked him to stay on until mid-January.
Maharaj would not comment on the inquiry into the misappropriation of the pension money.
The Cape Times said the Godongwanas owned 50% of the shares in the company through a family trust.
Inquiry
Godongwana appeared before the inquiry late last year, but his evidence could not be reported as there was a possibility of him being recalled to give further testimony.
The inquiry was expected to resume this month.
It has so far led to two arrests - those of former pensions consultant Richard Kawie who, with Mohan Patel owned through family trusts the other 50% of shares in Canyon Springs; and Sam Buthelezi, who was the sole director of the black empowerment asset management company, Trilinear Capital.
Kawie reportedly facilitated the loan, which was invested by Trilinear, the Cape Times said.
Godongwana has denied being aware that clothing workers' provident fund money was involved in the loan made to Canyon Springs.
Economic Development Minister Ebrahim Patel's spokesperson Saleem Mowzer said the minister would not comment on the matter.
He referred all queries to Maharaj, saying: "The presidency is dealing with it."
Godongwana is a member of the ANC's economic transformation committee.
He was previously the deputy minister of public enterprises and served as a member of the provincial legislature in the Eastern Cape.
Democratic Alliance spokesperson Kobus Marais welcomed Godongwana's resignation.
"It does, however, raise questions about whether the deputy minister was pushed out of office before all the investigations into his actions have run their full course," he said.
Godongwana still needed to be held fully accountable for his involvement in Canyon Springs, and the investigations by the police and the public protector should continue until the true extent of "his involvement is established", Marais said.
http://www.news24.com/SouthAfrica/Politics/Last-day-for-Deputy-Minister-Godongwana-20120116
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