Players shoot onscreen enemies using a gun controller. Virtua Cop 3 introduces a new slow-motion "bullet time" mechanism called "ES mode" which allows players to slow down time by stepping on a special pedal. While in ES mode, time slows down as the player's ES meter is depleted. The meter can be replenished by shooting more enemies.

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Virtua Cop 3 also allows players to toggle between different weapons by pressing a button on the gun instead of having to use just one weapon, as in previous entries in the series. The alternative weapons include the Smith & Wesson Model 629, Benelli M4 Super 90, H&K MP7, and the H&K G36C. Like the previous installments, players progress through the game choosing between three missions which vary in difficulty. The newly designed gun used in the game is named the Guardian II, and was designed by Tokyo Marui, famous for their model guns.