The UN Development Programme has urged Guatemala to overcome what it called "historically racist attitudes" towards indigenous peoples.
The UN says some advances have been made on literacy and health
Unless Guatemalans end this situation, the country could become ungovernable, the UNDP report warns.
There are crucial social and economic differences between aborigines and people of European or mixed indigenous origins - known as Ladinos, it added.
Maya Indians make up about 50% of population - most live in poverty.
According to the UN report, on average the Ladino majority in Guatemala earns more than twice the monthly income of their indigenous counterparts.
The report also highlighted problems such as poor transport links in parts of the country which are mainly inhabited by indigenous people.
The UNDP warned that should the government fail to act, "the country will become increasingly hard to govern".
Last year, five Guatemalan politicians were found guilty of racial discrimination against indigenous activist and Nobel Prize winner Rigoberta Menchu.
However, the UN body also highlighted some advances made for the aborigines in the 10 years between 1994 and 2004, particularly in terms of literacy and health.