Edinburgh University found the drugs may also affect the fertility of future generations, by leaving marks on DNA.
Experts said the findings added to growing evidence some medicines, including Paracetamol, should be used with caution during pregnancy.
Researchers stressed advice for pregnant women remained unchanged.
Current guidelines say, if necessary, Paracetamol should be used at the lowest possible dose for the shortest possible time. Ibuprofen should be avoided during pregnancy.
The study looked at the effects of Paracetamol and ibuprofen on samples of human foetal testes and ovaries.
The scientists found similar effects using several different experimental approaches, including lab tests on human tissue samples and animal studies.
Human tissue exposed to either drug for one week in a dish had reduced numbers of germ cells that give rise to sperm and eggs, cells, the study found.
Ovaries exposed to Paracetamol for one week had more than 40% fewer egg-producing cells. After ibuprofen exposure, the number of cells was almost halved.
Experts said this was important because girls produce all of their eggs in the womb, so if they are born with a reduced number it could lead to an early menopause.
Painkiller exposure during development could have effects on unborn boys too, the study found.
Testicular tissue exposed to painkillers in a culture dish had around a quarter fewer sperm-producing cells after exposure to Paracetamol or ibuprofen.
The team also tested the effects of painkiller treatment on mice that carried grafts of human foetal testicular tissue.
The grafts have been shown to mimic how the testes grow and function during development in the womb.
After just one day of treatment with a human-equivalent dose of Paracetamol, the number of sperm-producing cells in the graft tissue had dropped by 17%. After a week of drug treatment, there were almost one third fewer cells.
Previous studies with rats have shown that painkillers administered in pregnancy led to a reduction in germ cells in female offspring. This affected their fertility and the fertility of females in subsequent generations.
The scientists found that exposure to Paracetamol or ibuprofen triggered mechanisms in the cell that made changes in the structure of DNA, called epigenetic marks.
The marks can be inherited, helping to explain how the effects of painkillers on fertility may be passed on to future generations.
Painkillers' effects on germ cells are likely caused by their actions on molecules called prostaglandins, which have key functions in the ovaries and testes, the researchers found.
The study, published in Environmental Health Perspectives, was funded by the Medical Research Council, Wellcome and the British Society of Paediatric Endocrinology and Diabetes.
Dr Rod Mitchell, who led the research at the University of Edinburgh's MRC Centre for Reproductive Health, said: "We would encourage women to think carefully before taking painkillers in pregnancy and to follow existing guidelines - taking the lowest possible dose for the shortest time possible."