Poland could face legal action and EU penalties for failing to "adequately protect" its natural habitats, a European Commission official has said.
Poland is home to many rare species including bears
EC biodiversity expert Agata Zdanowicz said Poland had so far failed to comply with the EU's Natura 2000 programme, describing the situation as "serious".
The Commission started an "infringement procedure" against Poland in April.
This could lead to a court case and the blocking of EU funds for projects in Poland's environmentally fragile areas.
Natura 2000 is an EU-wide programme to safeguard the 25-nation bloc's most important wildlife areas and species.
Half of Europe's mammal species, one-third of reptile, amphibian and fish species, as well as one-third of plant species are threatened with extinction, according to the World Wildlife Fund (WWF).
Poland is home to rare species such as bison, wolves, bears and eagles living in river valleys, wetlands and forests.
The Commission rejected Poland's proposals on Natura 2000 earlier this year, describing them as "significantly insufficient".
The proposals did not comply with the EU's Birds and Habitats directives, Ms Zdanowicz, policy officer at the EC's nature and biodiversity unit, told the BBC News website.
Poland designated 72 sites as special protection areas under the Birds directive, but Ms Zdanowicz said the Commission was pushing for 140 such sites.
She said the situation was particularly "serious" with the implementation of the Habitats directive, which protects plant and animal species other than birds.
She said Warsaw had so far failed to "adequately protect" some 85% of such sites.
In April, the Commission launched the infringement procedure against Poland by sending it a written warning.
Poland formally responded in July, and Ms Zdanowicz said EC experts were currently analysing the amended proposals.
Both the EC and Polish officials are refusing to elaborate on the content of the new proposals, but Ms Zdanowicz said the EC could take the case to court if it deemed the plan to be inadequate.
Polish Environment Ministry spokesman Slawomir Mazurek told the BBC News website that "some mistakes" had been made during the development of Natura 2000 for Poland.
"Some areas have been appointed without a detailed knowledge of what is in them. Local governments do not agree on many of those areas," Mr Mazurek said.
He added that the ministry submitted to the EC what he described as "a repair programme".
Last week, Polish Prime Minister Jaroslaw Kaczynski reignited the row by hinting at a possible downsizing of the programme.
"Natura 2000 has expanded so much that it is practically impossible to build anything," he said.
His statement drew criticism from environmentalists, who said Poland needed to take urgent steps to protect its environment.
Natura 2000 protects 18% of land in the 15 countries that formed the EU before the expansion in 2004.
The size and number of protected sites is currently being negotiated for each of the 10 new member states.
The Commission has already warned 13 EU states over non-compliance with the bloc's environmental directives.