In order to control potential negative impacts arising from manufacturing activities, Jababeka has established a specific department for environmental management, which is in charge of monitoring the discharge of industrial waste water, hazardous materials and toxic waste (B3 waste). In addition, this department also monitors ambient air quality, waste management, and oversees the implementation of AMDAL (analysis of environmental impact) at plant and management level as well as in the industrial and residential area.

In addition, Jababeka has built a waste water treatment center with the use of German technology, which ensures that the discharged waste water meets environmental standards. Jababeka has also established a laboratory, which fully supports the environmental management activities, not only waste water treatment but also with the purpose of monitoring air and sound pollution as well as pollution of groundwater and rivers. In 2005, National Accreditation Committee (KAN) accredited the Jababeka Environmental Laboratory, which means that its results of analysis are recognized in the Asia-Pacific region.