Zuma said he was still paying a bank bond for the five family buildings that form part of the compound.
The Mail & Guardian erroneously reported that Defence Minister Nosiviwe Mapisa-Nqakula said on Tuesday the president's rural residence would receive further upgrades to the clinic situated on the premises.
It was in fact that the clinic would receive "minor adjustments" to serve the Nkandla community along with Zuma and personnel designated for his protection.
"Having assessed both the location and size of the clinic facility, it is our view that, save for minor adjustments, the clinic has adequate capacity to serve both the requirements of the president whenever necessary as well as provide for the community of Nkandla," Mapisa-Nqakula said.
The minister said discussions were already underway with the Kwazulu-Natal department of health to effect the decision.
Details of the additions to the clinic were not provided by the minister, however Mapisa-Nqakula reiterated all upgrades were solely on the basis of providing added security at the Zuma's Nkandla residence.
A briefing with the minister's special advisor Mike Ramogoma on Wednesday revealed that the additional work carried out at the the clinic would not be extensive.
"It certainly doesn't mean there will be additional works carried out at the clinic or anywhere else at the residence," he said.
Upgrades to the president's private residence at Nxamalala in rural Nkandla have become a bone of contention since it was reported that over R200-million would be forked out for infrastructural improvements.
The project is chiefly financed by the public works department with the last payment reportedly taking place days before President Jacob Zuma called for financial caution in light of current economic conditions – along with a pay freeze for senior public and private sector executives.
Additions to the property include a helipad, medical clinic, bulletproof glazing and air-conditioning in certain residential units as well as a bunker.
The upgrade is currently the subject of an investigation by public protector Thuli Madonsela, although a public works' report on alleged abuse of public funds during the upgrades found no signs of wrongdoing.
Mapisa-Nqakula also said on Tuesday that there is no evidence that any funds were used to build the "actual houses" of the president, as they were already at "completion level" when he was sworn into office in 2009.
The Mail & Guardian apologised for errors in its previous report.