Speaking to the BBC, Flint said: "We are lucky in the sense that we have a major bank in France.
"So, if we were to leave and if there were to be restrictions, ultimately on the renegotiation of Britain's position, we have the ability to move activity and people between London and Paris," the BBC Radio 4's Today program.
Commenting on the bank's decision to remain headquartered in London, Flint warned the result of the referendum "potentially does have an impact on the operating activities of our wholesale bank".
"Our strong economic view is that Britain is better within a reformed Europe," he said.
The Hongkong and Shanghai Bank employs around 10,000 people in France compared to 48,000 in Britain out of a global workforce of 257,000.
Prime Minister David Cameron is headed to Paris to meet French President Francois Hollande on Monday on a crucial week culminating in a summit in Brussels where he is hoping to renegotiate Britain's EU membership.
Opinion polls indicate a close race between supporters and opponents of Britain staying in the EU and big businesses have voiced concern about the impact from the uncertainty ahead of the vote.