The former world champion was surprisingly dropped by the peloton on the short late climb on stage 3 and finished nearly nine minutes down on stage winner Fabio Aru.
As he climbed onto the Team Sky bus he spoke to Cyclingnews, his voice barely audible as he tried to recover from a tough day in the saddle.
“It was very difficult out there today,” he said. “I don’t know how the stage finished. It was just a very, very difficult day.
"I think I’m on the way to preparing for the Tour and the rest of the season. I’ve made a nice programme and I felt great on the first and second stages but today I felt a bit sick in my lungs. I don’t know what it is but I need to see the doctor.”
Kwiatkowski, 26, has had an up and down debut season at Team Sky. He won E3 Harelbeke but failed to deliver in the Ardennes Classics.
The Pole had been brought into the team in order to deliver one-day success and form part of Chris Froome’s core Tour de France squad. He has spent time in recent months training with Froome and other members of the team at altitude.
“I’ll carry on in the race but I hope it’s nothing serious,” he said as he sat on the steps of the team bus.
“I lost my voice and have a cough in my lungs. Other than that I think I’m where I need to be.”
Froome currently sits third in the overall standings, 13 seconds down on race leader Alberto Contador. Kwiatkowski added that he would fight on and help his team leader throughout the remainder of the race.
“In the coming days I’ll do everything that I can for Chris. We came here with him for GC.”