The Swedish government was informed of the incident around ten years ago but no action was taken.
SVT's Uppdrag Granskning programme reports the existence of three top secret files within the military security service MUST detailing the incidents.
The reports - from November and December 1999 and June 2000 - state that the Russian military is suspected of dumping sensitive material overboard on repeated occasions between 1991 and 1994.
The chemical weapons and radioactive material are reported to have come from the vast Karosta naval base in the Latvian city of Liepaja.
The Swedish defence forces informed the government about the suspected dumping at a security meeting with representatives for the Swedish security services (Säpo), the National Defence Radio Establishment (Försvarets radioanstalt – FRA), Swedish Customs Agency (Tullverket), the Swedish Agency for Non-Proliferation and Export Controls (ISP) and MUST.
The information did not lead to any action being taken.
Neither the Ministry of Defence, the Ministry of Foreign Affairs nor the Prime Minister's Office retains reports of the dumping.
According to an SVT source, Bertil Lundin, one of Sweden's most prominent spies, passed the information on to the Ministry of Foreign Affairs informally.
Sven Olof Pettersson, political advisor to then foreign minister Anna Lindh, was asked how much Lindh had been told about the incident.
"That the Russians had dropped ammunition and chemical weapons into the Baltic Sea in modern times," he replied.
According to Sven Olof Pettersson, she became "very angry" and wanted the matter investigated. But she was told by the Ministry of Defence that without knowing the exact position it would be too expensive to search a large expanse of the Baltic Sea.
"For this to have been done in the 1990s is very different from if it had occurred in the 1940s or in the beginning of the 1950s. Then there were no international regulations; international environmental issues did not have at all the same focus as as they did in the 1960s and 70s," Jonas Ebbesson, professor in environment law at Stockholm University, told SVT.
"The most important thing now is not to find someone to blame. The most important thing is to locate the dumped barrels and identify their contents," Rolf K. Nilsson, Moderate MP for Gotland, said in a press release.
Nilsson argues that it is not just a Swedish matter, even if the barrels were dumped in the Swedish economic zone of the Baltic Sea.
"If the details of the dumping are correct then it is something that affects all of the Baltic Sea states," Rolf K.Nilsson says, adding that now is a very good opportunity for Russia to demonstrate its good will.
Anatoly Kargapolov, press officer at the Russian embassy in Stockholm was unwilling to comment on the reports until the matter had been thoroughly investigated in Moscow.