JPS Federal Territory of Labuan was established in 1992.
In the early establishment, JPS WP Labuan was part of JPS Wilayah Kuala Lumpur where all expenses, administration, and affairs were handled through JPS Wilayah Kuala Lumpur.
The previous office of JPS WP Labuan was located in the Building of the Public Works Department WP Labuan.
Subsequently, in 1993, JPS WP Labuan office relocated to the Saguking area of WP Labuan to further facilitate the department's tasks/functions at that time.
And in the year 2001, once again, JPS WP Labuan office relocated to the 5th floor, Block 4, Kompleks Ujana Kewangan, WP Labuan.
This department applied to become a department in a state, which was approved by the JPS Headquarters and the Ministry of Natural Resources, Environment and Climate Change (NRECC). Therefore, in 2007, JPS WP Labuan became a new branch in the Jabatan Pengairan Dan Saliran.
On April 3, 2017, another historical was recorded when JPS WP Labuan commenced operations in its own building located at the JPS Complex, Rancha-Rancha Road. The office of JPS WP Labuan represents an upgrade from workers' quarters to an office.
The functions and roles of JPS WP Labuan are as follows:
a. Water Resources and Hydrology Management
b. River Basin Management
c. Coastal Zone Management
d. Flood Management
e. Eco-friendly Drainage
f. Mechanical and Electrical Engineering