One of the plants, in Hsinchu City, is scheduled to begin trial operations in the middle of this month and provide 9,000 tonnes of water per day to the city by the end of this month, the agency said in a statement.
Construction of the other plant, in Kaohsiung, is almost complete, it said, adding that the plant is likely to begin trial operations by the end of the month.
Limits on water use remain in effect in parts of Taiwan, particularly in the south, where reservoirs have received little to no rain since September last year.
On March 24, the Executive Yuan approved a plan to supply an additional 136,000 tonnes of water to southern Taiwan per day through better water management and newly drilled wells, among other measures.