According to the WAPOU, as of April 13, the prison muster reached more than 5500 prisoners for the first time - 1000 more prisoners than the system is designed to hold.
Canning Vale-based Hakea Prison had 950 inmates in a prison designed for 745.
WAPOU secretary John Welch said with the State Government having a "tough-on-crime" agenda, more cells needed to be built to accommodate the extra prisoners.
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READ NOW"When prisons are overcrowded, prisoners are more likely to become violent and that is putting prison officers at greater and greater risk," he said.
Two units at Hakea Prison were being cleared out, taking another 128 cells out of the system.
"It will make the overcrowding crisis at Hakea worse, and the overflow of prisoners will have to be moved to Acacia, which will worsen the overcrowding there as well," Mr Welch said.
A recent report by the Australian Bureau of Statistics showed WA had the second highest imprisonment rate in the country.
A Department of Corrective Services spokeswoman said claims the state's prison system was overcrowded were inaccurate and prison numbers were consistent with forecasted trends.
"The occupancy rate of beds is below the nationally accepted limit," she said.
"This allows the Department to maximise the efficiency of the prison while retaining flexibility to manage daily fluctuations in prisoner numbers. Prisoners can be moved to other available beds as part of standard prison management practices.
"Some prisoners from one unit of Hakea Prison have been relocated to available beds in other fully staffed units."
The Department's estate optimisation plan will include a 387-bed expansion at Acacia Prison and the new 350-bed Eastern Goldfields Regional Prison. The projects are part of a $655-million capital investment program.