The Foreign Ministry said in a statement posted on Twitter that the provocative act hurts many people and creates a division between different religions and cultures.
Despite religious freedom in Denmark, many Danish citizens are Muslims. "They are a valued part of the Danish population," the statement stated.
The country believes that freedom of expression and assembly must be respected, it said, adding that "Denmark supports the right to protest but emphasizes that it must remain peaceful."
On Friday, members of the Islamophobic and far-right nationalist group "Danske Patrioter (Danish Patriots)" burned a copy of the Holy Quran in front of Iraq's Embassy in Copenhagen, Denmark.
Earlier this week, Salwan Momika, a 37-year-old Iraqi refugee living in Sweden, stomped and kicked the Holy Quran, just weeks after he set fire to pages of the holy book outside a Stockholm mosque.
While in January this year, Rasmus Paludan, a far-right Danish leader, burned a copy of the Quran in front of the Turkish Embassy in Stockholm. The incident sparked outrage and condemnation across the Islamic world.
A Turkish court has issued an arrest warrant for Paludan following his Islamophobic act. The investigation launched by the Ankara Chief Public Prosecutor's Office against Paludan on the charge of "publicly insulting the religious values" is ongoing.
As part of the investigation, the Chief Public Prosecutor's Office requested Paludan's arrest to obtain a statement regarding the Quran-burning incident.
The Ankara 8th Criminal Court of Peace, upon evaluating the request, decided to issue an arrest warrant for the Danish politician.