Ibuprofen affects the production of sex hormones and prolonged use could also lead to muscle loss and depression, they found.
While taking it for an occasional headache is unlikely to cause a problem, many people turn to the drug for long-term pain management.
Sufferers of chronic arthritis and athletes with persistent injuries are among those who rely on it.
Scientists tested the effects of the equivalent of six 200mg Ibuprofen tablets on volunteers, and studied testicle cells.
They said protracted use could lead to a condition called overt primary hypogonadism, which affects the sex hormones that regulate the production of testosterone.
The research team, from the University of Copenhagen, warned: “Ibuprofen appears to be the preferred pharmaceutical analgesic for long-term chronic pain and arthritis. Therefore, it is also of concern that men may eventually progress to overt primary hypogonadism, which is characterised by low-circulating testosterone and prevalent symptoms including reduced libido, reduced muscle mass and strength, and depressed mood and fatigue.”
Dr Richard Quinton, senior lecturer in endocrinology at Newcastle University, said: “This study should give pause for thought to sportsmen using them routinely for exercise-induced aches and pains.”
John Smith, of the Proprietary Association of Great Britain, said: “This small-scale study analysed the results of 31 male patients aged 18 to 35, of which 14 subjects were administered two 600mg daily doses of Ibuprofen for six weeks - significantly longer than is recommended for over-the-counter medicines.
“It is worth noting that during the trial none of the participants reported any adverse effects from taking the medication.”