Shareholders in the London Stock Exchange are due to vote on a planned merger with its German counterpart Deutsche Boerse.
The two agreed a $27bn (£20bn) deal earlier this year but the Brexit vote has raised questions about how it should be implemented.
Both companies have said the outcome does not affect the logic of the deal.
However Germany’s regulator, Bafin, said the headquarters could not be in London, as had been planned.
“Without doubt… it is hard to imagine that the most important exchange venue in the eurozone would be steered from a headquarters outside the EU,” said Felix Hufeld, Bafin’s president.
“There certainly has to be an adjustment here.”
It does not have a veto on the deal but it is thought that Deutsche Boerse is likely to take its concerns seriously.
In a joint statement released shortly after the UK’s referendum the companies said the outcome did not affect “the compelling rationale of the merger”.
In fact, the head of the Deutsche Boerse Joachim Faber said the decision made it “ever more important to maintain and foster ties between the UK and Europe”.
The deal still needs to be approved by regulators and, according to Reuters news agency, any major changes to it could need further shareholder approval.
As it stands, the deal is expected to be approved later on Monday with German shareholders due to vote on it on 12 July.
The companies hope to complete the deal in early 2017.