Within the activities of the NEMO project, the installation of a 8-floors tower (NEMO-Phase II) at a depth of 3500 m is foreseen in 2012. The tower will be installed about 80 km off-shore Capo Passero, in Sicily. On board the NEMO tower, an array of 18 acoustic sensors will be installed, permitting acoustic detection of biological sources, studies for acoustic neutrino detection and primarily acoustic positioning of the underwater structures. For the latter purpose, the sensors register acoustic signals emitted by five acoustic beacons anchored on the sea-floor. The data acquisition system of the acoustic sensors is fully integrated with the detector data transport system and is based on an "all data to shore" philosophy. Signals coming from hydrophones are continuously sampled underwater at 192kHz/24 bit and transmitted to shore through an electro-optical cable for real-time analysis. A novel technology for underwater GPS time-stamping of data has been implemented and tested. The operation of the acoustic array will permit long term test of sensors and electronics technologies that are proposed for the acoustic positioning system of KM3NeT.