Emeny said he hoped services could begin soon.
Air Chathams has operated scheduled and charter flight services to many of New Zealand's smaller communities, including the Chatham Islands, since 1984.
A small group of spectators at Kapiti Coast Airport watched on Tuesday morning as the last Kapiti passengers boarded an Air New Zealand plane, and the service left in grey overcast conditions.
One of the spectators was Eileen Shaw, who has regularly watched the service since it started on Labour Weekend 2011.
"I feel sad for me, but I feel for the people who now have to go to Wellington or Palmerston North to catch a plane [to Auckland].
"This airport is so local and so lovely.
"I'm going to miss it [watching the planes] so much.
"Someone said, 'it's just a load of metal', but I said, 'no it's a beautiful lady on the tarmac'."
Air New Zealand had invited Shaw to a luncheon at Raumati Beach later in the morning.
And in a nice touch, she was given a "Fly Kapiti" T-shirt by Kapiti Coast District Council's Janice McDougall.
Kapiti acting mayor James Cootes said it was disappointing to see the last flight but new opportunities would be created.
"As one door closes another one opens."