"It cannot be said for sure that this step introduces sanctions against Nord Stream 2 or that it will never be launched", the minister told German Deutschlandfunk broadcaster.
In another statement, the official said that there has long been an "illusion" that the project can be considered only from the perspective of economic policy, as energy issues is now linked to security.
"It would be smarter not to build Nord Stream 2, since we need a varied and diverse energy landscape in Europe, and not a concentration of risks in the Baltic Sea", the politician told German ARD broadcaster.
Earlier in the day, Habek said the Nord Stream 2 project, which is to transport Russian gas to Germany, could be halted due to the situation around Ukraine, with Berlin coordinating actions with European and American partners.
On Tuesday, German Chancellor Olaf Scholz instructed the country's economy ministry to take a "necessary administrative step" in order to suspend the certification of the Nord Stream 2 pipeline operator. The measure followed Russia's recognition of the Donbass republics - DPR and LPR.