While the UK's bio-pharmaceutical industry says it is committed to reducing and ultimately replacing the use of animals for scientific research, "this is not yet possible due to the complexity of the interactions between cells, tissues, and organs in the body, which cannot yet be fully modeled in vitro or by computers," Dr Virginia Acha, ABPI executive director for Research Medical and Innovation told CNBC via email.
Repealing the existing EU directive would halt development of new life saving medicines, she added.
As of 2011, 11.5 million animals were being used for testing across Europe. Official EU data suggests that nearly half the amount of animals used in 2008.
But Stop Vivisection's proposal raises concerns that the EU's existing laws are unnecessarily re-using animals for experiments, inflicting severe pain.
Read More Johnson & Johnson to consult ethicists on requests for experimental drugs
In an emailed statement to CNBC, German pharma giant Bayer insisted that their own animal research practices are kept to a minimum and that lab animals face no undue stress.
"Europe already has some of the strictest and most well-developed regulations around animal testing around the world," IHS Life Sciences director Gustav Ando told CNBC.
Companies would simply move their operations elsewhere, to countries where both standards and research quality was lower, UK-based health research charity Wellcome Trust warned in a statement to CNBC.
"It would seriously undermine Europe's attractiveness as a location for scientific and medical research," a spokesperson for the Wellcome Trust told CNBC by email. They said rolling back existing laws would "damage EU prosperity."
Some leading figures in pharma research and development have already left Europe due to security risks after being targeted by animal activists, Ando said.
Read MoreThe right to try experimental drugs gets more transparent
Rodents and rabbits currently account for over 80 percent of the total research animals used in the EU. Mice alone represent 59 percent, and rats 17 percent.
Stop Vivisection's appeal was launched as a European Citizens Initiative (ECI), which prompts the European Commission to consider new laws as long as they're backed by at least 1 million citizens from seven of the EU's 28 member states.
The Commission will have until June 3 to issue a formal reply to the group, and outline whether they will move forward with legislation to ban animal testing completely.
Stop Vivisection did not reply to CNBC requests for comment by press time.
Follow us on Twitter: @CNBCWorld