"This is no more than a joke. Provinces have no powers over civil aviation matters," Civil Aviation Minister Priyankara Jayaratne said a day after the resolution was adopted by the Council controlled by the main Tamil party TNA.
The resolution called for the establishment of direct air links between northern Jaffna peninsula's Palaly and eastern province's Trincomalee with India.
Jayaratne said: "The country has only two international airports and the approval for any more international airports must come from the government and not from provincial administrations."
Shivajilingam also moved two more resolutions - to convert the Kankesanturai port in Jaffna to be a commercial port and to urge for the recommencement of the ferry service between Talaimannar in the north and Rameshwaram in India.
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The ferry service was halted in 2013 after being in operation over a brief period.
The Northern Provincial Council had also adopted a resolution calling for an international probe into alleged war crimes committed by the Sri Lankan troops during the final phase of the battle against the rebel Tamil Tigers.
The LTTE was vanquished by the military in 2009 after nearly three decades long ethnic war.