Named after Kunhali Marakkar, the 16th century naval chief of the Zamorin (Samoothiri) Hindu king of Calicut, Marakkar Watermanship Training Centre (MWTC) is located in Kavvayi backwaters, inside INA campus.  Watermanship/ Seamanship training is the most important and an integral part of the naval training curriculum.  MWTC holds more than 200 boats of various types (both, power and sailing boats included) for conduct of training.MWTC imparts training to cadets and officer trainees in boat handling, sailing, pulling and other water sports viz., rowing, kayaking, canoeing and other waterborne activities.  The cadets are taught about basics of pulling, sailing and power boat handling in their initial terms.  The cadets are gradually graduated to Enterprise Class for sailing.  The interested cadets also learn sailing of Lasers, 26er and hobby cat. The cadets’ professionalism of sailing is put to test during the inter-squadron championships where in they compete in sailing, pulling and rowing categories. 
These competitions are conducted with an aim for maximum participation and exposure to the cadets in the water sports.  Further, these competitions form very important aspect for cadets as the winning points will aggregate towards champion squadron banner. The camps form a one of the important evolutions in any military training institution.  Being a waterborne force, the camps at the academy are designed in such a way that the cadets are exposed to open sea conditions and acquire the sea sailing experience.  The class room instructions on watermanship are put to use during camps to the fullest. MWTC coordinates an international sailing event Admiral's Cup Sailing Regatta (for cadets and officer trainees of friendly foreign navies) at the picturesque Ettikulum Bay.  With a view to enhance Indian Navy's cooperation with Navies of the world, this international sailing regatta is conducted every year since Dec 2010 conducted as a fleet race in a single crew Olympic class 'Laser-Radial' sail boat. In the fifth edition (2014), 17 countries from across the continents participated and the numbers are increasing every year. Apart from this the Indian Navy has instituted the ‘Open Laser Championship'’ to promote the sport of sailing in India. This event is also coordinated by MWTC at Ettikulum Bay. Sailing teams from the three services and all major sailing clubs in the country were invited to participate in the event. The participants had competed in sailing at the Ettikulum Bay on 'Laser-Standard' and 'Laser-Radial' class of sail-boats for cumulative prize money of over half a lakh rupees. The championship is being conducted under the aegis of the Indian Naval Sailing Association (INSA).  Both these events are conducted annually in December every year. These events also provide national level exposure to the cadets of INA. The MWTC has received its accreditation from the YAI.