Swedish Environment Minister Andreas Carlgren said his country was "aware of Germany's needs for that gas ... and that it is necessary for Europe to find other ways to get gas from Russia and to get gas and energy from several sources.
"But that can in no way interfere into our legal process," he told reporters at a breakfast meeting in Brussels.
German Chancellor Angela Merkel on Thursday urged EU backing for three new European gas pipeline projects, including the Nord Stream pipeline in question.
Merkel said these projects were important to diversify both the sources and routes of gas supply to the European Union following a crisis between Russia and Ukraine that hit central Europe and the Balkans earlier this month.
However the Baltic states and Poland have objected to Nord Stream, concerned at being bypassed by a major Russian gas supply route to Europe, which depends heavily on Russia for energy.
Sweden's misgivings on Friday were environmental.
"Parties or companies like Nord Stream have the right to make use of the sea to build pipelines, but on the other hand there is an obligation for coastal states to make sure that they won't face unacceptable environment consequences," Calgren said.
"So far Nord Stream has not presented full and sufficient quality documentation for the environmental impact," he stressed, adding that this was a concern for the Baltic states not just Sweden.
The Swedish minister said they were now awaiting fresh information in March, after which it would take at least three months to study whether they fill all the environmental gaps.
Construction of the pipeline could disturb heavy metals present in the sediment and chemical weapons dumped in the Baltic Sea, Sweden's Environmental Protection Agency has said.
The Nord Stream gas pipeline, which concerns nine nations, is a partnership between Russia's state-owned gas monopoly Gazprom and German giants E.On and BASF-Wintershall.
The Nord Stream consortium agreed in 2005 to build a 1,200-kilometre undersea pipeline from Vyborg in Russia to Greifswald in Germany, aiming to turn on the taps by 2010 to supply energy-hungry Western Europe.
It will at the same time bypass countries such as Ukraine, Belarus and Poland whose relations with Moscow have been strained.
The pipeline is due to be built between 2009 and 2011.