Harassment of Christians in asylum centres, social pressure against circumcision, intimidation of religious minorities and religion-related terror attacks were all cited as causes for concern in the Scandinavian country.
Denmark received a slap on the wrist for its record on religious freedom in four separate reports, writes news agency Ritzau.
The latest of the reports was released by American research centre Pew earlier this month.
The Pew reports states that religious freedom in Denmark regressed significantly between 2007 and 2015, leaving the country amongst Europe's worst 25 percent of countries in the area.
“Denmark experienced in 2015 several religion-related terror attacks, an escalation in relation to previous years,” Katayoun Kishi, head researcher on the Pew report, told Ritzau.
“In August 2015 an assailant threw a Molotov cocktail at a mosque in Copenhagen, and in February that year Omar Abdel Hamid al-Hussein attacked a cultural centre that was hosting a debate on freedom of speech and synagogue during a bar mitzvah,” she added.
Denmark, which is named in the highly-regarded report for the first time, is also criticised for a 2014 law change forbidding ritual slaughter of animals without anaesthetic as well as increased pressure against the right to circumcise baby boys.
Other organisations that have called out Denmark on religious freedom include Catholic NGO Aid to the Church, which stated its concern about harassment of Christians in Danish asylum centres.
A 2016 UN reported also criticised the Church of Denmark as well as the concept of ‘Danishness' as being exclusive towards religious minorities, according to the Ritzau report.
Brian Arly Jakobsen, professor in religion and politics and the University of Copenhagen, told newspaper Kristeligt Dagblad that the criticism of the Danish church might be closely related to its unusual status compared to many other countries.
“The high score on state discrimination is due to the high status of the Church of Denmark, which gives it privileges that other religions don't have. This is classified by Pew and others as being a restriction on religious freedom,” he said.