It seems that you belongs to innies who are prone to have this issue. Here are details:
In most cases, what determines if your navel will smell when it isn’t being properly washed and cared for is its shape. In some people, their navels face upwards while some others have navels that face inwards. The two unconventional names for these two types of navels are outies and innies. The navel is located at one spot in your body where both dirt and oil accumulate; bacteria live in it most times. Mostly, the innie-styled type of navels is most prone to bacteria growths, which explains the characteristic disgusting odor that emanates from them. Outies may still be prone to bacteria growth, but to a much lower degree. The link below will help you learn how to get your bellybutton cleaned properly.
http://www.enkivillage.com/how-to-clean-belly-button.html
In some rare cases however, a number of skin problems can worsen cases of navel odor and the production of bacteria. Skin conditions like eczema can increase the number of dead skin cells which flake off to clog up the navel. This kind of skin condition can encourage the growth of bacteria and oils thereby causing more smells.