"Following an assessment of the doubts expressed in the protests of the applicants, and a new comprehensive environmental review, the previously issued permit remains valid", BSH said in a statement.
The statement in defence of the project was issued after earlier in the day operator Nord Stream 2 AG said that 95 percent of the gas pipeline was complete.
In January, German environmental organisations Deutsche Umwelthilfe and NABU lodged a protest over BSH's decision to extend the permit for Nord Stream 2 pipelaying work.
While the pipeline's construction is approaching completion, Nord Stream 2 is still facing pressure from the US, with Washington planning to slap new sanctions on the project in a bid to stop its launch.
The US has been claiming (since the Trump administration) that Nord Stream 2, a joint project by Russia's Gazprom and EU energy corporations, will undermine European energy security, while Moscow and the EU consider these efforts to be an instance of unfair competition.