The soil chamber technique is most commonly used for measuring gas exchange between soil surfaces and the atmosphere, to understand regulatory processes relevant to determine the greenhouse gas (GHG) emissions from soils and to improve the emissions inventory of agricultural systems. The chambers are inserted into the soil to avoid the lateral diffusion of the gases. However, soil disturbance caused by chamber insertion causes in degassing and can result in erroneous flux data from measurements made immediately following chamber insertion. Here we assess the effect of soil disturbance associated with the insertion of the chambers on nitrous oxide (N2O) and methane (CH4) fluxes with and without N fertilization, from a New Zealand pasture soil. We collected gas samples from the chambers at 0, 2, 4, 24, 96 and 168 h after chambers insertion. Our results show elevated levels of N2O inside the chambers (1.7 fold those of atmospheric concentrations outside the chambers) and greater fluxes within the first 4 h of installation compared to the values observed at 24 h and later; and negative CH4 flux in the same time period, but near to zero after 24 h. Our results suggest that for accurate measurement of gas fluxes, measurements should be taken after 24 h of chambers installation to avoid the degassing effect.