Chief Government Chemist Laboratory was established in 1908 as a small laboratory under the Ministry of Health, in 1925 it was shifted to the Ministry of Agriculture in which its duties were related to researches on crops such as cloves, spices, fruits, soil analysis and livestock products especially milk and industrial products. Police cases and Forensic chemistry were later included among the activities performed by the laboratory. In 1994, the laboratory was shifted back to the Ministry of Health.

Chief Government Chemist Laboratory is one of the oldest laboratories in Zanzibar and East Africa as a whole with an age of over 100 years. It started as small unit with three staff through ministerial department to an Agency with seventy four staff.

The laboratory was located at Mnazi Mmoja and in 1992 it was transferred to Livingstone building after the collapse of the ministry building. In 1994 the laboratory was transferred to Mwanakwerekwe where it became an executive department until 2011 when it was officially changed into an agency. In 2013 it was shifted to Maruhubi industrial area formally a cigarette company about 5 km from Zanzibar town.