The inaugural service will cover Ashtamudi Lake in Kollam district and Punnamada Lake in Alappuzha district. Cessna 206 amphibious aircraft will be used for the inaugural flight.
The state aims to connect at least 25 tourist destinations under the service. In the first phase, it plans to connect Ashtamudi, Punnamada, Vembanad lakes and the backwaters of Kochi and Kottappuram.
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Houseboats would serve as terminals at the landing and take-off sites with lounges for tourists. Seaplanes will be allowed only to take the aerial route and operations will be limited to day time.
Tourism minister A P Anil kumar said: "To start with, there would be one service daily, however, it would be increased later. We reject the apprehensions of the inland fishermen community as the service doesn't affect fishing in the lakes and back waters."
The seaplane service was among the project ideas showcased at the 'Emerging Kerala Global Connect' event held here last year.