The Italian official spoke out on Monday, which was designed the “International Day of the World’s Indigenous Peoples”.
There are around 300 million indigenous people in 70 countries throughout the world - five per cent of the world's population.
The international day was established by the United Nations in 1994 to promote the rights of the world's indigenous population. This year, the theme is 'Indigenous Peoples' Right to Education'.
According to the UN, "indigenous peoples have the right to establish and control their educational systems and institutions providing education in their own languages, in a manner appropriate to their cultural methods of teaching and learning."
Speaking on Monday, Mogherini said she wanted to mark the “richness” of other cultures and their “unique contributions” to the world's cultural diversity.
The Italian official added, “The EU reaffirms its commitments to promote and protect the rights of indigenous peoples.
“Despite the many positive developments in recognising the rights of indigenous peoples, there are persistent human rights violations, including killings and abuses against indigenous human rights defenders in a range of countries.”
The High Representative also announced that the EU was stepping up its efforts to protect human rights defenders working for the “most vulnerable and marginalized”, including indigenous peoples, and those campaigning on land rights issues.
She said, “The EU is also stepping up its engagement with indigenous peoples, in line with the EU action plan on human rights and democracy.”
Before the end of the year, the EU intends to prepare an overview of its policies and actions supporting indigenous peoples as well as a list of best practices, she added.
“The promotion of cultural rights in accordance with the UN Declaration on the Rights of Indigenous Peoples is also at the heart of peace-building.”
In June, the Organisation of the American States adopted the “American Declaration on the Rights of Indigenous Peoples.”
It is the first instrument of its kind that specifically addresses the rights of the indigenous peoples of the Americas.
“The declaration will add a new dimension to the EU's relations with its partner countries in the Americas,” said Mogherini.
Meanwhile, the EU and UNICEF have agreed to broaden a partnership that aims to protect children from violence and better include children with disabilities into society.
Since 2011, the EU and UNICEF have been working together with countries currently in the process of joining the EU, such as Albania, Bosnia and Herzegovina, Serbia and Turkey.
On Monday it was announced that this partnership is now expanding to include Kosovo, Montenegro and the former Yugoslav Republic of Macedonia.
As of this year, the NGO European Disability Forum (EDF) has also joined the partnership.
Johannes Hahn, European neighbourhood policy and enlargement negotiations Commissioner, said: "We believe that this partnership can make a real difference to the life of children in the region.
“We rely on UNICEF's and EDF's expertise and knowledge to influence policies that have an impact on children who are victims of violence and children with disabilities.”
The official added, “ At the same time, it is crucial to reach out to civil society and grass-root organisations working on child protection and to promote children inclusion in societies.
“Therefore, a large part of the funding will be devoted to support small civil society organisations to achieve real change and sustainable improvements of children's daily life and future perspective."