Schleck had been accused in some quarters of abandoning the race in Italy early with a view to better preparing for the Tour de France.
Bruyneel was reported to be disappointed with Schleck and even considering dropping the Luxembourg rider for the event in June.
But in an interview carried on the team's official website, Schleck attempted to put those rumours to bed.
"I believe some people have misunderstood what Johan Bruyneel has said in the press," Schleck said.
"He said that the results of the team are disappointing and that none of our leaders can automatically claim a post in the Tour. Johan has not said that I'm not going to do the Tour.
"We have had a long and good talk after I withdrew. The next morning, on the rest day, we had another very good talk. He was disappointed, just like me.
"We decided to prioritise my recovery and then start building up again. He was very respectful and we talked about a lot of things. I left Italy with a really good feeling."
Schleck withdrew from the Giro less than an hour into stage 15 with pain in a shoulder injury sustained a day previously.
The severity of the blow had been called into question, but when asked if he had pulled out to concentrate on his preparations for the Tour de France, he said: "I can firmly tell you that this is not true.
"I gave it everything I could. Why would I drop out of a race that was almost finished, to change my program and do the Tour of Luxembourg and the Tour de Suisse instead? It makes no sense.
"Those are very hard races, so they are not ideal in a Tour preparation. You know, I was supposed to have a month of specific training - so no racing - after the Giro. It's just not logical to drop out just before the end and do two hard races instead."
Schleck is due to return to hospital for further tests on his shoulder and also his leg, which he says is inflamed from overcompensating his painful shoulder with a cramped position on his bike.