The Commission says that Germany's approach breaks EU rules on cross-border trade and restricts people from other countries doing business in Germany and with German firms.
The Commission has begun proceedings against Germany despite the fact that the country has promised to change the rules.
The Commission said that German patent and trade mark law says that anyone seeking to take action via its patent and trade mark office must use a patent agent with an address in Germany.
"The Commission takes the view that such a requirement is disproportionate and obstructs the freedom to provide services as guaranteed under Article 49 of the EC Treaty," it said.
"The Commission has noted the intention of the German authorities to amend the rules concerned. However, in view of the delay in adopting the amendments and the continued existence of an infringement, it has decided to send a reasoned opinion," said a Commission statement.
A reasoned opinion is one stage in the Commission's formal legal process of taking countries to task over failures to implement EU law properly.
"The purpose of the reasoned opinion is to set out the Commission’s position on the infringement and to determine the subject matter of any action, requesting the Member State to comply within a given time limit," said the Commission's explanation of the process.
The reasoned opinion is the second stage in the process. If no reply meeting the Commission's satisfaction is sent within two months then the Commission can take action in the European Court of Justice (ECJ).