Sir Dave Brailsford says Team Sky can be trusted "100%", despite "regrettable" questions over Sir Bradley Wiggins' medical records.
Wiggins and Team Sky boss Brailsford have come under scrutiny since information on the rider's authorised use of banned drugs to treat a medical condition were released by hackers.
There are also questions over a medical package he received in 2011.
"Can people believe in Team Sky? 100%," Brailsford told the BBC.
UK Anti-Doping (Ukad) has been investigating allegations of doping in cycling after it emerged a mystery medical package was delivered to a Team Sky doctor for Wiggins on the final day of the 2011 Criterium du Dauphine, which the Briton won.
Brailsford, the former performance director of British Cycling, last month told a parliamentary select committee he understood the package contained a legal decongestant, Fluimucil.
Ukad chairman David Kenworthy last week told BBC Sport he found the evidence of Brailsford and British Cycling president Bob Howden "extraordinary", saying the answers to the select committee on the content of the medical package were "very disappointing".
But when this was put to Brailsford, he answered: "The only extraordinary thing I could see was that he [Kenworthy] actually commented on the whole process himself.
"There is an open investigation that is still ongoing."
Wiggins, 36, announced his retirement from cycling last month. Britain's most decorated Olympian's use of therapeutic use exemptions (TUEs) came to light after his confidential medical information was leaked by hackers 'Fancy Bears'.
TUEs allow the use of otherwise banned substances if athletes have a genuine medical need, and Wiggins, who has asthma, said he took them to "put himself back on a level playing field".
There is no suggestion Wiggins, British Cycling or Team Sky have broken any rules.
"It is regrettable," added Brailsford. "But equally the test of time is the key thing, and over time we will continue to perform at the highest level, continue to do it the right way, continue to give people a reason to get behind us and feel proud of our achievements.
"The judgement of what happened in the past will be made in the appropriate time, but for me we have done it the right way, and we'll continue to do it the right way.
He added: "I'm proud in what I've done, I've been doing this a long time, and I've been doing it for 20 years. I'm very much focused on the season ahead."