Katainen, who met with Polish counterpart Donald Tusk this week in Gdansk, said the countries have made strides on ridding the heavily trafficked Baltic of phosphorous, which causes choking algae and has created large "dead zones" on the sea bottom.
However, he said, more needs to be done to bring the sea back to environmental health and preserve fish stocks.
"Our main challenge relates to removing phosphorus from municipal and industrial waste waters as it causes blue-green algae," he said. "Due to the sensitive nature of the Baltic Sea, the phosphorus levels must be lower than the targets set by the EU.
"It is a challenging objective but we want the future generations to have a cleaner Baltic Sea."
Tusk added the Baltic's salmon population needs to be protected, the Polish news agency PAP reported.
"Our common concern is the state of the environment, especially when it comes to the Baltic Sea," he said. "This issue is of particular concern to Finnish fishermen and our country will participate in European research in order to obtain an objective assessment of how together we can take care of the salmon population in the Baltic Sea."
The Baltic is plagued by nitrates and phosphates from waste run-off.
The nutrients, contained in fertilizers and sewage, enter the sea from large "spot" sources such as wastewater treatment facilities and also from diffuse sources, such as scattered farm fields.
Environmentalists say the pollution is causing the "eutrophication" of the Baltic Sea, though which algae blooms deplete oxygen from the water, triggering fish die-offs and creating a 25,000-square-mile "dead zone" -- an area the size of Latvia.
A 2007 action plan developed by the Helsinki Commission of nine Baltic Sea nations has achieved a 40 percent reduction in direct nitrogen and phosphorus discharges as well as a 40 percent decrease in airborne nitrogen emissions.
But to achieve its stated objective of eliminating the Baltic's algae blooms, direct phosphorous and nitrogen inputs must be cut a further 42 percent.
Katainen praised Poland's efforts to control waste run-off into the sea.
"I know Gdansk, Szczecin and Warsaw have invested in new wastewater treatment plants, which have already have done a great job," he told PAP. "We want to think about what else Poland and Finland can do together to reduce pollution."
Baltic region environmentalists also remain concerned about Russia's push for two more Nord Stream gas pipelines, joining two existing lines running 760 miles across the seabed. They are worried the construction will stir up toxic chemicals contained in the seabed sediment.
But Katainen said Finland wouldn't be opposed to future pipelines "if they will not have a negative impact on the Baltic Sea.
"We need more energy in Europe and one of the ways of obtaining it is building connections with Russia," he said.
The two leaders also talked about new investments in clean energy technology, part of a larger effort to boost Finnish spending in Poland.
"We have a very strong economic cooperation and clean technology is the strongest sector of industry, which is now being developed in Finland," Katainen said. "Renewable energy and biofuels are areas where Finland is very strong and is very interested in investing in Poland."