A system for the real-time and fully automated detection, classification and localisation of acoustic sources in the marine environment has been developed at the Laboratory of Applied Bioacoustics (LAB) of the Technical University of Catalonia (UPC). The system features modules for the detection, the classification and localisation of short tonal sounds and impulsive sounds and the quantification of the level and the spectral characteristics of the background noise. The system has been successfully validated for the detection of many sound-types from fixed ocean cable observatories (ESONET, ANTARES, NEPTUNE). In particular, the detection module for short tonal sounds has been effectively applied to detect baleen whales and delphinid calls and whistles. The system is operational on live acoustic data streams from fixed ocean observatories (www.listentothedeep.org), demonstrating its ability to handle continuous data streams with a sampling frequency as high as 250 kHz. Here, we applied this module for the detection of short tonal sounds has been adjusted to detect calls of baleen whales in acoustic data from the sea floor observatory off Kushiro in the Kuril Trench, Japan (www.jamstec.go.jp/scdc/top_e.html). This data was recorded at a sampling frequency of 100 samples per second. The detector was first validated on data series from several marine observatories that were either known to contain Fin Whale calls or to be from regions where Fin Whales do not occur. The 384 hours of acoustic data used off Kushiro ranged from 25 th April to 10 th May 2010 without gaps. Many sections of these recording contained in the frequency band intense impulsive noise, or interferences, from unknown anthropogenic sources. Nevertheless, the system successfully detected a train of Fin Whale calls that occurred on April, the 29 th 2010 between 02h15-03h15. The call showed a frequency down sweep in the range 30-15 Hz with duration of 1-2 seconds. The signal to noise ratio of these calls, as perceived by an experienced operator, was clearly lower than in the validation data sets. This demonstrates (1) that Fin Whale are present off Kushiro, (2) that the detector can handle calls with a very low signal to noise ratio and (3) that the real-time automated detection of baleen whale calls can be performed live at JAMSTEC network of observatories.