The Institute for Accountability in Southern Africa launched the complaint after a July report in The Times exposed the crisis at Charlotte Maxeke Johannesburg Hospital.

In the article, doctors said the bed shortage forced them to "play God" and choose which children were accepted into the unit and which were sent to a general ward.

Paul Hoffman, director of the institute, said yesterday the complaint to the protector followed "unsuccessful attempts to engage with the Department of Health and the relevant parliamentary committee on this issue".

Department of Health spokesman Fidel Hadebe disputed this: "I am not aware of who exactly in the department the institute has been interacting with, without any success, but as far as I know the department interacts with a range of civil society organisations, right from the minister himself all the way down."

The department admitted to a national shortage of paediatric beds in intensive care units. It was reported last year that 750000 children under the age of five die in South Africa every year.

"Discretionary state expenditure, which is so often wholly unnecessary, unused, and wasteful, should not be allowed to compromise the effective and efficient delivery of the socioeconomic rights [that are] set out in the constitution, but nowhere to be seen almost a generation after the liberation of the South African people," said Hoffman.

The public protector's spokesman, Kgalalelo Masibi, did not respond to confirm the investigation yesterday.