The presidency said Köhler has decided not to add his signature to the embattled reform treaty pending its ruling on applications seeking to block ratification.
"Given the urgent applications waiting to be heard, the president is respecting a request of the Constitutional Court," his office said.
The adoption of the Lisbon Treaty is being challenged by The Left, a radicial left-wing opposition party, and a member of the ultra-conservative Christian Social Union, Peter Gauweiler.
Gauweiler, who also challenged the EU constitution, the ill-fated predecessor to the Lisbon Treaty, argues that the new text is not compatible with the country's democratic principles and has launched an urgent application preventing the signature.
The Left is contending that the EU itself lacks democratic legitimacy and that the treaty -- which seeks to streamline decision-making in the bloc -- is seeking to lock Europe on a neo-liberal economic course for generations to come.
The upper house of the German parliament approved the Lisbon Treaty on May 23 before passing it on to Köhler for his signature -- which is usually a formality. The lower house passed it in late April.
German Chancellor Angela Merkel was seen as one of the champions of the text and has, along with French President Nicolas Sarkozy, called on member states to keep it alive by continuing ratification after Irish voters rejected it in a referendum on June 12.
The Irish vote plunged the EU into a new constitutional crisis as all 27 member states must approve the text before it can enter into force.
Nineteen nations have ratified the Lisbon Treaty in parliament, most recently Britain. Ireland was the only EU member to hold a referendum.
Britain was able to complete ratification after London's High Court last Wednesday rejected a legal bid to force the government to hold a plebiscite to approve the text.