With Britain set to leave the single market, imports from the UK will need to be declared upon arrival in Germany.
The same is true to exports to Britain after the country leaves the union in 2019.
This will cost Germany tens of millions of pounds, something already causing concern in Germany.
The country’s Finance Ministry said: “Even in the best case – a very far-reaching free trade agreement – there will be customs controls again between Great Britain and Germany.”
A government source said they expected 14 million registrations for exports and 2.7 million for imports.
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Eric Schweitzer, president of the German Chamber of Commerce and Industry said he expected these registrations to cost €200 million (£178 million).
He said: “True free trade in goods exists only in the single market.
“Therefore after Brexit the cost of bilateral trade with Britain will definitely increase, whether with a free trade agreement or just with WTO rules.”
And the Federal Association of Wholesale and Foreign Trade (BGA) admitted Brexit would be increasing “bureaucracy” in Germany.
BGA President Holger Bingmann said: “The additional bureaucracy that German companies are facing is considerable.”
It comes after a business chief pleaded with Britain not to leave the EU, joking: “You are the only country with common sense left – please stay!”
Hans-Olaf Henkel told a Brexit conference in London in November Germany and the rest of the EU will suffer if Brexit goes ahead, especially with no exit deal agreed.
Mr Henkel is the former president of the Federation of German Industries (BDI) which includes hundreds of companies and organisations.
He said: “Let me tell you at the outset: I do not know one person in BDI that wants Brexit. The situation is quite clear. We need the best deal possible for Britain – and that will also be the best deal for Germany.”