His comments came as chief executive Stuart Gulliver admitted HSBC's global reach left it vulnerable to criminal networks.
Giving evidence to the Parliamentary Commission on Banking Standards, Mr Flint defended banks' practices of paying top employees a bonus that can be many multiples of their basic salary.
He said: "I think used properly it is very powerful for the good."
Since the financial crisis, the banking industry has faced accusations that the lure of high bonuses encourages staff to take large risks.
However, Mr Flint said that paying a bonus meant the bank could demand its staff act in accordance with certain values, as well as meet performance standards, before qualifying for the bulk of their expected pay.
Some awards cannot be cashed in until retirement.
Mr Flint said: "This gives protection both to shareholders and to the company and to the system generally, so we cannot create a circumstance where people get rewarded today because it looks terrific and in the future years it does not."
However Pat McFadden, the Scots-born MP for Wolverhampton South West, told Mr Flint the banking industry's approach to pay and widespread of use of bonuses is "completely weird".
He noted that footballers such as Barcelona player Lionel Messi also receive large pay packages.
Mr McFadden said: "They are exceptional awards but I also know they are exceptional sportsmen who would be difficult to replace, and in the case of Messi impossible to replace."
But, he said, as for bankers, "they are more replacable than they think".
HSBC's pay arrangements have avoided some of the hostility seen elsewhere, with even a £7.2 million award to chief executive Stuart Gulliver for 2011 being waved through by shareholders last year.
It did not require a state bailout during the financial crisis although it did raise £12.5 billion from its shareholders.
However, it faced multi-billion-pound losses on its sub-prime lending business in the United States.
In December it was given a $1.9bn (£1.2bn) fine, the largest ever imposed on a bank, following a US investigation into money laundering breaches at its Mexican and US operations.
Mr Gulliver said: "Our geographic footprint became very attractive to trans-national criminal organisations, whether they are terrorist in origin or criminal in origin. We've crushed our reputation with the Mexico events.
"The behavioural stuff of what went on in Mexico is absolutely shocking to us."
The two bankers sought to convince the inquiry that the bank has changed, in part by selling off some less important businesses and centralising functions to make them easier to control.
Mr Gulliver, who became chief executive in 2011, said: "We have removed senior people from HSBC for values breaches on my watch."
Mr Flint, who described himself as "unashamedly an accountant", said bankers should move towards the professional standards seen in medicine and law.
"It is going to be very difficult to do but trying to create professionalism, where there is a broader duty that transcends the profitability of the firm, is really important."