This depends on which company you hire from. I collect my car at Heraklion Airport from Autotrip on arrival. The previous hirer returns the car at or near empty. If my flight is arriving early afternoon or evening I buy petrol at a station near the airport. On a late arrival I ask the company to put 25 - 30€ in for me, enough to get me to Rethymnon safely. I can then top up as needed at my local filling station.
Bear in mind fuel, with recent tax and duty rises, is now much more expensive in Crete than in UK, (see the thread on fuel costs on this board) and probably other European countries.