Although India has a long experience in ship-borne experiments and oceanographic instrumentation, the atmospheric component has not received much attention in the past. In this paper, the basis of the atmospheric instrumentation system assembled for use on board ORV Sagar Kanya for the BOBMEX-Pilot experiment is described along with some representative results. Wherever possible, Woods Hole's IMET recommendations for meteorological sensors for applications in the marine environment have been followed to keep our measurements in par with international standards. The sensors were tested during the BOBMEX-Pilot experiment and all sensors worked well. Velocity, humidity and temperature data have been successfully collected using fast sensors. It is shown that the component due to the ship's pitching motion can be removed from the measured vertical velocity by making use of an accelerometer. This makes it possible to calculate the surface fluxes by direct methods.