If you are connected to a municipal sewer system, yes...in reasonable amounts. Just make sure you're only flushing the waste, not the bag.
But if you are on a septic system, do not flush your pet's waste. Flushing pet waste can exceed the capacity of your septic system. The contents of your pet's waste, like grass, ash, and hair, can interfere with septic system functions and clog your drain field. In addition, your system is not designed to handle the hazardous organisms found in pet waste.