The basement archive in the Ministry of Defense appears to hold some records about Operation Condor, a coordinated campaign by South American military governments against leftists during the 1970s and 80s, according to rights activist Martin Almada.
The discovery was announced hours after Almada gained access the rows of boxes and yellowed ledgers on Wednesday morning. He said the documents apparently contain names of Argentine opponents of Stroessner's government.
"In skimming through them, we uncovered some interesting information regarding Operation Condor," said Almada, who directs a museum about past government repression and torture.
Several South American military governments are accused of working together to crack down on leftist dissidents beginning in the mid-1970s.
Many alleged "Operation Condor" abuses are being investigated for the first time after Argentina overturned legal amnesties and Uruguay elected its first leftist president.
Stroessner was toppled in a 1989 military coup, but the regime's allied Colorado Party held on to power until 2008.
President Fernando Lugo, a left-leaning former Roman Catholic bishop, has apologized on behalf of Paraguay to victims of the dictatorship. His government has promised to search for any common graves where Stroessner's opponents may have been buried.
According to Almada, the newly uncovered records will be reviewed by members of Argentina's Grandmothers of Plaza de Mayo, a human rights group formed by people whose children and grandchildren were abducted by government agents and disappeared during the "dirty war" there.
"Many relatives of disappeared prisoners don't know where their loved ones are buried. Maybe these documents will provide clues," Almada said.
The archives also included reports dating back to the 1932-1935 Chaco War that Paraguay waged and won against Bolivia, including the names of thousands of Bolivian prisoners.
Paraguay's Museum of Memory displays photos of the people that disappeared along with torture tools used under Stroessner's rule.