The Sunday Times journalist was speaking to The Pat Kenny Show
Team Sky are in crisis, with reports that General Manager Dave Brailsford may leave the team.
Sunday Times journalist David Walsh travelled with the team at their peak, writing the book Inside Team Sky. He told The Pat Kenny Show that his view of the team has changed recently as Team Sky continue to move from one scandal to another.
"I believed in them," Walsh admitted. "I have no difficulty in accepting that, if that's a criticism.
"How do I feel now? I feel Dave Brailsford was dishonest with me. Sometimes you can be dishonest by omission."
Walsh revealed that he would not have travelled with the team writing the book, if he knew Brailsford was fully honest with him about Therapeutic Use Exemptions, and he has since told the Team Sky boss that.
"What I said was; 'Dave, if you had told me in 2013 when you were inviting me into the team - if you had told me that you had given Bradley Wiggins TUEs before the 2011 Tour and 2012 Tour, I wouldn't have offered to spend time inside the team. I would have wanted to investigate that first.'
"His argument was; 'Well those TUEs were approved'. I said; 'Why didn't you tell people about them? Why the secrecy?' It turns out that the secrecy was because they knew if they consulted their other doctors, those doctors would have caused a stink."
Team Sky used TUEs on 2012 Tour de France winner Bradley Wiggins twice before the race. Walsh is unsure why Wiggins received one.
"The thing about Wiggins that made people suspicious was that he got one in 2012. He just won the Criterium du Dauhpine, which is the number one preparation race for the Tour de France. He pretty much won every race that year. He was in the form of his life and the health of his life... There was no hint of him being sick.
"In hindsight, should I have been suspect about going inside the team? I think that's fair, and maybe I should have been."
While Walsh has lost all faith in Brailsford, he feels there are still "good people" within Team Sky.
"Having being inside the team, I got to know people. I got a pretty good understanding of the kind of people that are in there. I was definitely wrong about Dave Brailsford. What I know now has changed my view on the part he has played, but I do know there are a lot of good people in that team."