Environment Minister Andreas Carlgren told reporters on Tuesday that the application was so incomplete that he did not consider it worthwhile sending it on to the relevant authorities.
"Effectively we're just sending it straight back to them," he said.
As well as a gas pipeline running from Russia to Germany, Nord Stream also intends constructing a service platform some 40 kilometres east of the Swedish island Gotska Sandön.
Nord Stream hopes to begin work on the pipeline in 2009 but the Swedish government said it was refusing to make any decision until a full environmental impact analysis had been carried out.
"We're not even going to begin considering the matter until the application has been completed," said Carlgren.