In an interview with public broadcaster Polish Radio, Anna Moskwa said that "the blooms of the algae" could produce toxins that kill fish and clams.
She added that the microorganisms were not harmful to humans.
Moskwa told Polish Radio that an investigation was under way into the causes of "the extensive blooms of the algae."
"The drought, low water levels and weather conditions have no doubt contributed to the situation, but experts are investigating additional factors," she said.
She added that "illegal sewage discharge or technical malfunctioning have been ruled out."
Moskwa also said in the interview that initial reports of the presence of mercury as the cause of the contamination of the river "have not been confirmed."
Iwona Jasser, a researcher at the University of Warsaw, has said in a comment that the term "golden algae" covers a wide variety of species, most of which are not toxic.
However, they also include the toxic Prymnesium parvum variety, and so further research is "a major challenge for experts," Jasser told Poland's PAP news agency.
Moskwa told a news conference earlier this week that there were several hypotheses as to the causes of the mysterious mass die-off of fish in the Oder River, which also flows through Germany.
She said at the time that the environmental disaster "may have been caused by a toxic substance entering the Oder; by unfavourable natural conditions; by a large amount of industrial wastewater being dumped into the Oder, causing notable salinisation of the river; or by a combination of hypotheses two and three."
Poland's Main Environmental Inspectorate (GIOŚ) "has analysed water samples and none of them contained any toxic substances,” Moskwa told reporters on Wednesday.