Biogas upgrading is a vital step to produce high quality fuel called biomethane with above 90% methane (CH4). Among the various technologies available for biomethane production, water scrubbing is the most extensively implemented technology around the world. However, during the process of biogas upgrading, a some amount of CH4 is separated as CH4 loss through the water flowing out of the water scrubbing column. In this paper, various factors affecting CH4 loss from water scrubbing method are analysed. Some factors such as pressure, water flow rate and CH4 concentration in input gas are dependent upon the solubility and partial pressures of the gases are generally known. Apart from these factors CH4 losses due to bubble entrainment due to high pressure difference between water scrubbing column and desorption tank and gas short circuiting of the gas through the bottom section of the column due to no water sealing and water level maintencence also contribute to CH4 losses. Therefore, CH4 losses during the water scrubbing process due to these factors have been experimentally studied in this paper. A pilot scale water scrubbing system for biogas upgradation was used for the study. It was observed that CH4 % (v/v) in the upgraded biogas and CH4 loss % from the desorbed gas increased with the increase in pressure and increase in the concentration of CH4 in the input gas. Increase in water flow rates caused removal of larger quantities of water containing more absorbed CH4 and CO2 from the scrubbing column, thereby increasing CH4 loss of the system. Highest CH4 loss % of 9.9% (+/- 0.1%), was obtained with raw biogas sample when water was desorbed at atmospheric pressures in the desorption tank, i.e. when pressure difference between the water scrubbing column and desorption tank was highest. A pressure vessel was installed in between scrubbing column and desorption tank to reduce the pressure difference for water leaving the column by varying the pressure in the pressure vessel from 1 to 9 bar. With the increase in pressure in the pressure vessel, the pressure difference for water decreased which led to a saving in overall CH4 loss of the system. Water sealing and water level maintenance in the bottom section of the column also affected CH4 losses of the system. All the factors discussed in the article contribute to the CH4 losses from the scrubbing column and cannot be solely credited to a single factor.