If the gas is igniting every three minutes it's getting a signal to produce more heat. You may have problems in the electrical board that interfaces between the thermostat and the ignition system.
If it's just the fan coming on, that's different. The fan motor is controlled by the temp inside the box, not the thermostat. When the flame goes out, the fan will run until the temp drops but often the heat retained in the box will heat it up again enough to restart the fan.
If it continues to do that when you know for sure the heat in the box has expired, check the thermister and circuitry that controls the fan. Don't defeat it for any reason, it's made that way for safety.
An improperly operating gas system can be very dangerous. It might be worthwhile to have a professional look at it.