Antonio Horta Osorio said he agreed with most of the changes announced by the Bank of England last week, which will enable firms to claw back bonuses up to seven years after the award, and will require top bankers to be vetted every year.
"But the new rules will potentially reverse the burden of proof where individuals are guilty until they prove themselves innocent in the eyes of the regulator," he told Sky News.
"I worry that this could incentivise people to do nothing, as they could waste their time trying to create a paper trail rather than doing what they should be doing, focusing on customers."
Lloyds was last week fined £218 million for its role in rigging Libor and the firm is thought to be seeking clawbacks from 22 staff involved. It has also clawed back directors' bonuses in light of the rising bill for mis-selling payment protection insurance (PPI).
"We want to make sure that bankers, like any other profession, operate to the highest standards but we have to be fair in how we judge them," added Mr Horta Osorio.
A number of senior figures in finance have voiced worries about the deluge of new rules, including requirements to ringfence high street accounts from investment banks by 2019.
HSBC chairman Douglas Flint said on Monday that bankers were becoming too risk-averse to carry out legitimate business.