"We are not going to take a portion of the 160,000 asylum seekers to be distributed," Denmark’s Politiko web portal quoted Inger Stojberg as saying.
Stojberg cited Copenhagen’s non-signatory status to the Treaty on the Functioning of the European Union (TFEU), as well as the share of refugees for which it had originally committed, behind the rejection.
Denmark, alongside fellow non-signatories to the common immigration and asylum TFEU system United Kingdom and Ireland, is not required to adopt the measures proposed by European Commission President Jean-Claude Juncker.
Unveiling the updated proposal to the European Parliament on Wednesday, Juncker called on member states to accept the migrants over the next two years "in a compulsory way."
Local media quoted a center-right Venstre party spokesman saying this week the quota system is "not something we care for."
The UN Refugee Agency calculates Denmark had taken in over 17,700 refugees and nearly 4,300 asylum seekers as of December 2014.
The European quota system requests the resettlement of refugees among the bloc's members based on population, gross domestic product, average number of asylum applications and ratio of refugees to one million inhabitants, as well as the unemployment rate in the country.
The redistribution system seeks to relocate 54,000 refugees from Hungary, 50,400 from Greece and 15,600 from Italy.