Skeletons which have been dug up in the city during developments, some dating back to the Bronze Age, will now form a vital part of new research into TB.
Academics from Durham and Manchester universities have asked permission to remove bits of bone and teeth to analyse as part of their research project into how tuberculosis evolved through the ages.
The remains of two ancient city dwellers, one which is known to have suffered TB and one which did not, will be studied.
It is hoped their discoveries will lead to the formulation of new drugs to combat the disease, which is currently on the increase.
The samples will be removed by an expert using a small circular saw and taken to Manchester University for testing.
The dentine or yellow underpart of the teeth will be taken away, and the teeth returned to the museum service.
The bone samples will be destroyed but it is proposed they will be kept by Manchester University on loan from Portsmouth City Council.
Other councils which own human remains have already agreed for this research to take place and watchdog English Heritage has told Portsmouth City Council it is happy to permit the sampling for this research request.
Jennifer Macey, museums collections assistant at Portsmouth City Council, said: 'The remains will be treated respectfully throughout the sampling process.
'The potential benefits of the research will be a greater understanding of the evolution of tuberculosis in Britain and Europe, possibly being able to identify whether particular strains of TB have always occurred in certain regions or whether this is due to modern factors.'
The council's collection of human remains was examined last year by a student from University College London as part of a dissertation into changes in health in Hampshire during the Anglo-saxon period.
Samples were also taken during 2002 and 2003 by a researcher for carbon dating.
Hampshire, Winchester, Southampton and Chichester councils all hold human remains in their archaeological collections for research purposes.
Portsmouth City Council is now drawing up a policy for storing human remains in the museum collections which will follow government guidelines on ethics.