The legislation was approved by 42 votes in favour, none against and eight abstentions by the employment committee.
The proposal, which has already been informally agreed with EU ministers, sets EU-wide rules to eliminate and reduce all carcinogens and mutagens in workplaces.
Under the proposed text, employers will have to assess the risk of exposure for workers and take preventive measures.
MEPs on the committee said they believe this provision should tackle the primary cause of work-related deaths in the EU - cancer - with the aim being to help save up to 100,000 lives over the next 50 years.
Cancer is the leading cause of work-related deaths in the EU. Annually, 53 per cent of occupational deaths are attributed to cancer, compared with 28 per cent for circulatory diseases and six per cent for respiratory ones.
The most common types of occupational cancer are lung cancer, mesothelioma (caused by exposure to asbestos particles) and bladder cancer. The World Health Organisation (WHO) estimates that every tenth lung cancer death is closely related to workplace risks.
The committee was told that a recent study shows that more than one per cent of the workers are exposed to reprotoxic substances, which means that between two and three million could be affected in the EU.
The current legislative protection against such substances is limited to the general provisions of the chemical agents' directive, while the EU legislation on pregnant workers does not impose preventative measures. Exposure can reduce male or female fertility and cause death or malformations of foetuses.
The rules include a lower occupational exposure limit (OEL), in other words, a maximum quantity of harmful substances that workers can be exposed to.
Committee members said they wanted to ensure that the Commission will have to assess the possibility of including reprotoxic substances - those having effects on sexual function and fertility - by the first quarter of 2019.
The new rules adopted by parliamentary committee on Wednesday also state that national authorities can decide that health surveillance must continue after the end of exposure for as long as needed to safeguard health.
Parliament will put the draft directive to the final vote during one of the upcoming plenaries in Strasbourg.