He was hospitalised on Wednesday before midnight due to a recurrence of his lung infection, spokesperson Mac Maharaj said in a statement.
"Doctors are attending to him, ensuring that he has the best possible expert medical treatment and comfort," Maharaj said.
President Jacob Zuma wished him a speedy recovery.
"We appeal to the people of South Africa and the world to pray for our beloved Madiba and his family and to keep them in their thoughts," Zuma said in a statement.
"We have full confidence in the medical team and know that they will do everything possible to ensure recovery."
Maharaj appealed for "understanding and privacy in order to allow space to the doctors to do their work".
The admittance to hospital comes three months after the 94-year-old former president was admitted to hospital in the capital Pretoria on December 8, also for a lung infection and to remove gallstones.
His December stay was the longest since he was freed from Robben Island over two decades ago. He was discharged after 20 days and received home-based care.
Mandela has a history of lung problems after having suffered from tuberculosis towards the end of the 27 years he spent in prison.
Confusion over location
The government were heavily criticised in December for lying to the press and public about which hospital Mandela was being treated at.
The presidency declined to confirm a report that Mandela was not being treated in One Military Hospital as initially thought.
"The presidency has been consistent that [Mandela] is in a hospital in Pretoria and avoided identifying the precise hospital for reasons regarding the privacy for Madiba and his family," spokesperson Mac Maharaj said at the time.
He said this was to ensure his treatment was administered in the most conducive conditions for his recovery. "For those reasons we have avoided disclosing the precise hospital."
His comments came after a report on Eyewitness News report that Mandela was not receiving treatment at One Military Hospital in Pretoria.
In January, the presidency said Mandela had made a full recovery from the surgery and continued to improve.
In February 2012, he was admitted to hospital for a stomach ailment. At the time, the presidency said Mandela underwent a diagnostic procedure to investigate the cause of a long-standing abdominal complaint.
In January 2011, Mandela was taken to Milpark Hospital for routine tests relating to respiratory problems.
Mandela's last major public appearance was in July 2010, at the final of the Fifa World Cup at Soccer City stadium in Johannesburg.
Since then he had spent his time between Johannesburg and his ancestral village of Qunu in the Eastern Cape.
Additional reporting by Reuters.