We present the results of a variability study of accreting young stellar objects in the Chameleon I star-forming region which is based on ~300 high resolution optical spectra from the multi-object fibre spectrograph FLAMES/GIRAFFE at the ESO/VLT. Twenty five objects with spectral types from G2-M5.75 were observed 12 times over the course of 15 months. Using the emission lines Ha (6562.81 A) and Ca II (8662.1 A) as accretion indicators we found 10 accreting and 15 non-accreting objects. We derived accretion rates for all accretors in the sample using the Ha equivalent width, Ha 10% width and the CaII equivalent width. The mean amplitude of variations in derived accretion rate from Ha equivalent width was ~ 0.37 dex, from Ca II equivalent width ~0.83 dex and from Ha 10% width ~1.11 dex. Based on the large amplitude of variations in accretion rates derived from the Ha 10% width with respect to the other diagnostics, we do not consider it to be a reliable accretion rate estimator. Taking the variations in Ha equivalent width and CaII equivalent width accretion rates to be closer to the true value, they suggest that the spread which has been found around the accretion rate to stellar mass relation is not due to the variability of individual objects on time-scales of weeks to ~1 year. From these variations we can also infer that the accretion rates are stable within < 0.37 dex over time-scales of less than 15 months. A major portion of the accretion variability was found to occur on less than the shortest time-scales in our observations, 8-25 days, which is comparable with the rotation periods of these young stellar objects. This could be an indication that what we are probing is spatial structure in the accretion flows, and also suggests that observations on time-scales of ~a couple of weeks are sufficient to limit the total extent of accretion rate variations in typical young stars.