About 35% of adult South Africans are fully vaccinated, higher than in most other African nations, but half the government's year-end target. It has averaged 106,000 doses a day in the past 15 days in a nation of 60 million people.
Earlier this year the programme was slowed by insufficient doses. Now deliveries have been delayed due to oversupply.
Across Africa, vaccination rates are lower than much of the rest of the world, with many countries struggling to secure enough doses. But some countries are now seeing rising supplies while vaccine campaigns are not gathering pace, such as Kenya.
Nicholas Crisp, deputy director-general of the Health Department, told Reuters that South Africa had 16.8 million doses in stock and said deliveries had been deferred.
"We have 158 days' stock in the country at current use," a spokesman for the Health Ministry said. "We have deferred some deliveries."
They did not say when deliveries would now take place.
Stavros Nicolaou, a senior executive of Aspen Pharmacare, which is packaging 25 million doses a month of J&J vaccines in South Africa, said most of the vaccines bound for South Africa would now go to the rest of the continent.
Nicolaou, who is also chairman of public health at business lobby Business for South Africa (B4SA), said deliveries would likely be deferred until the first quarter of next year.
Vaccines packaged at Aspen's plant are part of the African Union's agreement to buy 220 million doses from J&J.
The AU and J&J did not respond to emailed requests for comment.
A Pfizer spokesperson said: "We remain adaptable to individual country's vaccine requirements whilst continuing to meet our quarterly commitments as per the South Africa supply agreement."
South Africa's government has been seeking to boost the rate of daily administered doses.
"There is a fair amount of apathy and hesitancy," said Shabir Madhi, who led the clinical study for the AstraZeneca COVID-19 vaccine in South Africa.
To ramp up vaccinations, the government has launched pop-up vaccination centres and sought help from community leaders. It has also opened inoculations to children aged 12 to 17.
In Kenya, the Health Ministry said on Sunday vaccinations were moving too slowly among some parts of the population. Its statement did not mention any plan to delay any deliveries.
"We are ... concerned that only 18% of the elderly population is fully vaccinated and that vaccine uptake has generally slowed down in several counties following the lifting of the curfew last month," Health Minister Mutahi Kagwe said.
(Reporting by Promit Mukherjee; Additional reporting by Maggie Fick; Editing by Josephine Mason and Edmund Blair)
By Promit Mukherjee