The amphibian service was flagged off by Chief Minister Oommen Chandy amid protest by traditional fishermen who claimed that it could pose a threat to their livelihood and marine ecology.
The maiden service between Ashtamudi Lake here and Punnamada in Alappuzha, however, was called off due to bad weather.
Marking its inauguration, the plane took off from the waterdrome and landed back.
Though it was proposed to take six passengers to Punnamada in the maiden flight, it was cancelled as weather contiuned to be hostile with the monsoon activity being vigorous.
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The service in due course envisages connecting the entire stretch of Kerala with Thiruvananthapuram, Kochi and Kozhikode airports, being base stations.
Allaying concerns of fishermen, who lined up a flotilla of fishing boats to register their protest on the occasion, Chandy said the service would not in any way affect their livelihood.
If they experienced any difficulty due to the seaplane's operation the authorities would examine it and take remedial steps, he said.
Union Minister of state for Civil Aviation K C Venugopal, state Tourism Minister A P Anil Kumar and Peethambara Kurup, MP, were present on the occasion.