"There is no scientific evidence to suggest that the lubrication of a condom can cure arthritis, and we are appealing to members of the public not to use condoms for any other reason than that for which they are intended," Health Minister Aaron Motsoaledi's spokesman Joe Maila told Sapa.
This was particularly the case given the severe problem with HIV and Aids in the country.
The Times reported that Mpumalanga's health MEC berated arthritis sufferers for rubbing condoms on their aching joints, believing the lubricant would ease the pain.
"She called on them to stop because condoms are meant for something other than rubbing on knees," MEC Candith Mashego-Dlamini's spokesman Ronnie Masilela was quoted as saying.
A Cape Town grandmother, who declined to be named, told The Times: "It is not a cure for my arthritis but it eases the pain."
A Johannesburg hiker said he put condoms over his emergency kit.
"My wife was really upset when she found the condoms but you can carry water in them," he told the paper.