Chief executive Juergen Maier said that while the German giant is committed to the UK, he is worried about the prospects for future investment.
"We are concerned about what the future might hold in terms of new investments that we might want to make" he said.
Siemens has 13 plants in the UK and employs about 14,000 people.
It manufactures and exports high value goods including MRI scanners and gas turbines.
His comments follow news that plans by Siemens to export wind turbine blades from a new facility in Hull have been put on hold.
The company's links with the UK go back 170 years. And Mr Maier, who campaigned for a Remain vote, insists that Britain is still a good place to do business.
"We are not going to run away from the British market. We are committed here. It's a great market," he told the BBC.
But he warned that the uncertainty which has followed the vote to leave the EU would soon have consequences.
He said: "Short term, in terms of any investment decisions you want to make here, especially those that result in exporting to the European Union, they will be on ice. No question about that."
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Investment decisions, he said, are a balance between factors including strong innovation and skills and how easy it is to trade.
"Unless you have a really strong argument for innovation or skills being particularly strong here, if those are similar to somewhere else the business case for investing here will now be less attractive until we know what the trading arrangement is going to be," he said.
The company is currently building a Â£310m manufacturing hub for wind turbine blades in Hull that will employ about 1,000 people.
Mr Maier insists that investment is safe and will continue. But plans to export from the facility in the future are now on hold.
"That's the opportunity that at the moment is not as clear," he said.
Mr Maier said that the UK government needs to get to work fast on a plan for how we will trade with Europe.
"We've got to make sure we end up in a situation where our relationship is strong and friendly with the European Union whilst accepting the democratic vote that we wont be..in the EU directly itself."
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One of the UK's biggest industrial companies, Siemens UK, has warned that investment could be hit in the wake of the Brexit vote.