Virkkunen made the remarks in response to statements by Baktash Siawash, a former Afghan lawmaker, at the European Parliament.
Siawash accused the European Union and the international community of applying double standards towards Afghanistan during Thursday's meeting. He called for the recognition of gender apartheid, an end to diplomatic relations with the Taliban and the group's designation as a terrorist organisation.
The European Commission's Executive Vice-President said the EU continues to support Afghan women and consistently criticises the Taliban's policies towards women and girls. She added that human rights violations, particularly the situation of Afghan women, remain among Brussels' main concerns.
Speaking at the meeting, Virkkunen said the European Union had not recognised the Taliban despite continuing to provide humanitarian assistance to Afghanistan. She explained that the EU had maintained its official presence in Kabul to monitor developments in the country closely.
She added that the EU's presence in Kabul did not constitute endorsement or recognition of the Taliban. Instead, its purpose was to engage with different sections of Afghan society and hear their perspectives, particularly those of women.
Describing the situation in Afghanistan as involving systematic human rights violations, Virkkunen said the EU's policy was based on engagement with the Taliban but stressed that such engagement should not be interpreted as recognition of the Taliban government.
She emphasised that maintaining contact allows the European Union to address issues including the formation of an inclusive government, combating drug trafficking and counterterrorism.
The senior European official also referred to ongoing discussions about using the term "gender apartheid" to describe the situation in Afghanistan, saying the European Union does not currently use the term.
Virkkunen said that we use the term gender-based persecution to describe the Taliban's treatment of women, but we are interested in and are following the legal and political discussions surrounding the concept of gender apartheid.
She added that meetings on crimes against humanity and human rights violations were expected to take place soon at the United Nations in New York, where the issue of gender apartheid would also be discussed.
The European Commission's Executive Vice-President further stressed that any future steps towards recognising the Taliban would first require substantial and measurable progress on women's rights and human rights.
According to her, combating terrorism and drug trafficking would also be among the important preconditions for any such move.
In another part of her remarks, Virkkunen highlighted efforts to establish an independent investigative mechanism for Afghanistan, saying the European Union had allocated funding to support its implementation.
She added that further financial contributions from EU member states and other countries could help strengthen accountability for human rights violations in Afghanistan.
Responding to Siawash's call for the Taliban to be designated a terrorist organisation, Virkkunen said the European Union had not currently listed the group as a terrorist organisation.
She explained that such a designation would require specific legal procedures and decisions by competent authorities in EU member states or partner countries.
Virkkunen also recalled that the European Union implements UN sanctions against individuals and entities linked to terrorism in Afghanistan.
She added that the EU had also placed five individuals on its human rights sanctions list for their involvement in serious violations of the rights of Afghan women and girls.