Jetta 1.9 TDI 2006 the cooling fan comes on five minutes after starting

you are low on gas so it will not click on as the gas is also the lubricant ,this vehicle should hold about 700 grms of gas

There should be a cooling fan relay, usually 1 for the engine and 1 for AC (might be labeled as secondary, or accessory.) I would check that next. A working relay will CLICK when activated. The fans are normally told to turn on by the PCM, which receives a signal from the coolant temperature sensor (CTS). It's possible the CTS is not sending the proper signal to the PCM, but I would first check the relays.

Check the fuse for the fan and you could test to see if you have a voltage running to the fan when the car starts to overheat. If you have no power to the fan then trace the wore and see if you cant find the problem. If you have power then the fan motor is most likely bad.

Hi it sounds like you have a temp sender playing up I think there are 3 on your engine,

When A/C is on, both fans should be on all the time. If one is not, probably a dead fan. Replace said fan.

fan relay control module and replace both high and low speed fans. and thats normal for the fans to come on with the a/c on thats what cools the ac condenser

With the key in the ignition (but not turned), press and hold the Odometer Reset Button on the right hand side of the panel. While still holding that button, turn the key (although not far enough to start the engine) and then press and hold the Minute button on the left side of the instrument pane(if pressing doesnt work try turning the knob clockwise until service light has gone off and skip the pressing)l. Release both buttons at the same time.

check your thermostat

My mechanic in our town did a quick computer check. Car computer indicated a low level of antifreeze, he topped it up, cleared all messages off the car computer and said to watch the the heat guage for any further irregularities. I'll keep an eye on it, love the car, great mileage fun to drive.

With key off press and hold the 0.0 button on the cluster. With your other hand turn the key on while still holding 0.0 button press the minute button 1 second and you will see the service reset.