An intensive investigation has been launched after a new born baby boy mysteriously disappeared from a hospital, hours after he was born, the Eastern Cape Health Department said on Friday.

Spokesman Sizwe Kupela said the baby was born in good health at the Dora Nginza Hospital in Zwide, Port Elizabeth on Thursday morning.

"The child was in the care of day nurses when he went missing at around 3pm.

"They [the nurses] said they never noticed that the child was not in the nursery.

"It was only the nightshift nurses who realised that one baby was unaccounted for ... they then alerted authorities."

Kupela said the department was working with a special task team of investigators and police in order to find the baby.

"We have since come across some information which may be crucial to finding the baby; CCTV camera recordings from Thursday are also being monitored," Kupela said.

He said the baby's 27-year-old mother was still in hospital as she underwent a caesarean section.

She was receiving counselling, he added.

"She is doing better today, but just wants her baby back in her arms."