We report measurement of low frequency 1/f noise in molybdenum di-sulphide (MoS$_2$) field-effect transistors in multiple device configurations including MoS$_2$ on silicon dioxide as well as MoS$_2$-hexagonal boron nitride (hBN) heterostructures. All as-fabricated devices show similar magnitude of noise with number fluctuation as the dominant mechanism at high temperatures and density, although the calculated density of traps is two orders of magnitude higher than that at the SiO2 interface. Measurements on the heterostructure devices with vacuum annealing and dual gated configuration reveals that along with the channel, metal-MoS$_2$ contacts also play a significant role in determining noise magnitude in these devices.