Despite their interest and threat status, the number of whales in world's oceans remains highly uncertain. Whales detection is normally carried out from costly sighting surveys, acoustic surveys or through high-resolution images. Since deep convolutional neural networks (CNNs) are achieving great performance in several computer vision tasks, here we propose a robust and generalizable CNN-based system for automatically detecting and counting whales in satellite and aerial images based on open data and tools. In particular, we designed a two-step whale counting approach, where the first CNN finds the input images with whale presence, and the second CNN locates and counts each whale in those images. A test of the system on Google Earth images in ten global whale-watching hotspots achieved a performance (F1-measure) of 81% in detecting and 94% in counting whales. Combining these two steps increased accuracy by 36% compared to a baseline detection model alone. Applying this cost-effective method worldwide could contribute to the assessment of whale populations to guide conservation actions. Free and global access to high-resolution imagery for conservation purposes would boost this process.