As long as the fan is a 12V fan you can use one of a number of solutions computer building enthusiasts use to control their case fans. One which might work for you is the following device:
This takes a 12V input, controls a 12V fan, and can be attached with the temperature sensor on the outflow of the case - whether near the fan or not. If connected to your transceiver it will be off and on as normal, but unless the temperature goes high it will reduce the fan speed. This means that it should be quiet except when the transmitter actually gets hot.
If you are interested in electronics, you can build one from a project like this PWM fan controller which is also temperature controlled. This project is more general, and can control fans that run at higher and lower voltages as well with the appropriate transistor (Q1). That site sells the parts required, and it isn't a particularly difficult build.
If you can provide the dimensions of the fan and other parameters (voltage, current, model number) then there may be other suggestions that would work.