We report a study of cloud cover over Indonesia based on meteorological satellite data spanning 15 years (from 1996 to 2010) to aid in the selection of a new astronomical site capable of hosting a multi-wavelength astronomical observatory. High-spatial-resolution meteorological satellite data acquired from Geostationary Meteorological Satellite 5 (GMS 5), Geostationary Operational Environmental Satellite 9 (GOES 9) and Multi-functional Transport Satellite-1R (MTSAT-1R) are used to derive yearly average clear fractions over various regions of Indonesia. This parameter is determined from temperature measurements in the IR3 channel (water vapour, 6.7 μm) for high-altitude clouds (cirrus), and from the IR1 channel (10.7 μm) for lower-altitude clouds. An algorithm is developed to detect the corresponding clouds. The results of this study were used to select the best possible sites in Indonesia, which will be analysed further by performing in situ measurements in the future. The results suggest that regions of East Nusa Tenggara, located in southeastern Indonesia, are the most promising candidates for such an astronomical site. The yearly clear sky fraction of this region may reach better than 70 per cent, with an uncertainty of 10 per cent.