The comments, made in a documentary which will be shown on BBC Two on Sunday evening, come in the week that UK Anti-Doping ended an investigation into alleged wrong-doing within British Cycling and Team Sky without bringing any charges.
In comments reported on the BBC Sport website, Sutton says on the documentary: "If you've got an athlete that's 95% ready and that little five% injury or niggle that's troubling them, if you can get that TUE to get them to 100%, then of course you would in those days.
"The business you are in is to give you the edge on your opponent. Ultimately, at the end of the day, it's about killing them off. But definitely don't cross the line and that's something we have never done."
Asked if the use of TUEs fit with Team Sky's mantra of "marginal gains," Sutton says: "Finding the gains might mean getting a TUE? Yes, because the rules allow you to do that."
Sir Bradley Wiggins received medical exemptions to use the banned drug triamcinoline at the 2011 and 2012 Tour de France, and the 2013 Giro d'Italia.
Wiggins - who became the first Briton to win the Tour in 2012 - had said the drug was necessary to treat his pollen allergies. He had described UKAD's investigation - which focused on the as-yet-unexplained contents of a jiffy bag delivered to Team Sky at the Criterium du Dauphine in 2011 - as a "malicious witch hunt."
Sir Dave Brailsford, British Cycling Perfromance Director speaks with Head Coach Shane Sutton on day three of the UCI Track Cycling World Cup at Manchester Velodrome on November 3, 2013 in Manchester, England.
Image credit: Getty Images
Team Sky principal Sir Dave Brailsford also features in the documentary, and said the TUEs granted to Wiggins were medically necessary and above board.
"I think if an athlete is hampered by an illness and there is a medication they can have and the TUE criteria is met then, yes, they should," Brailsford tells the programme, in comments reported by the Times and the Guardian.
"The doctor came forward and said, 'I think we have an issue here'. If Brad, the doctor and the consultant all say, 'That's what we think we should do', if (the World Anti-Doping Agency) and (the International Cycling Union) signed this off and it was all absolutely clear and above board, then I was comfortable with that."
Sutton is now head coach of China's track team, having left British Cycling in April 2016 following allegations of discrimination and bullying.
The documentary Britain's Cycling Superheroes: The Price of Success will be shown on BBC Two at 9pm on Sunday.