Team principal Dave Brailsford revealed the change of policy
Team Sky will in future reveal all cases where its riders have been given permission to use banned substances.
It follows the controversy over Bradley Wiggins' use of a powerful anti-inflammatory drug to treat breathing difficulties before his 2012 Tour de France victory.
Team principal Dave Brailsford revealed the change of policy as he offered a robust defence of the decision to seek three Therapeutic Use Exemptions (TUEs) for Wiggins to be injected with the corticosteroid triamcinalone in 2011, 2012 and 2013.
The TUE records were revealed in a leak of hacked data obtained from a World Anti-Doping Agency database by a Russian hacking organisation calling itself Fancy Bears.
Brailsford revealed that Team Sky has received 13 TUEs since its foundation in 2010, but in future they will make any future applications public with the consent of the rider.
He also suggested they might consider withdrawing any rider who was not willing to allow their medical details to be released in order to restore confident in the system.
Team Sky and Wiggins have been accused by experienced sports physicians and a number of current and former riders of abusing the anti-doping system to gain TUEs for a drug that many claim has powerful performance-enhancing qualities.
Questions have been raised as to whether Wiggin's physical condition in 2012 warranted the use of a drug that has been abused by cheats in the past. In interviews ahead of the 2012 Tour, and in his subsequent autobiography, he made no mention of breathing difficulties and said he was in peak condition.
Sky team director Sir Dave Brailsford poses for a portrait on the second rest day of the Tour de France cycling race in Sisteron, Tuesday, July 21, 2015. (AP Photo/Peter Dejong)
Brailsford has defended the process around all three of Wiggins' TUE applications, and insisted the team is "100% clean and does things in the right way".
He told Sky News: "Abuse is the key word. People have abused it in the past.
"But the question was, is there a genuine medical need, and given the process and the integrity of the process - there was a doctor and authorities who approved this - I didn't see any need to question this. I felt I could trust it.
He denied that the application was opportunistic, and intended as offering Wiggins "insurance" ahead of a race he was favourite to win.
"Not at all. The reality is that there was a requirement perceived therefore you go to a specialist, they say this is appriorpriate or it isn't. In that sense you have a confidence you have around the process."
Brailsford rejected the suggestion that despite Team Sky's public policy of zero-tolerance for doping, this episode revealed the team was willing to bend its ethical boundaries in order to win.
"I cannot agree with that. I get fierce scrutiny most of the time at British Cycling and Team Sky, whenever you perform well in our sport people put you under the microscope and we have had that time and time again at various stages of the way.
"What I can tell everybody is that we are doing it the right way. It is 100% a clean operation, we always look at the right thing to do and have policies and process to make sure that we perform in the right way and people can believe in us."
He also said it should not taint Wiggins' record.
"I hope not, he is a remarkable athlete who has achieved so much in his career and as you can see from his records he has not been a systematic abuse of TUEs, he has had very, very few. It would be very unfair to allow them to tarnish his career."