The report says the existing EU legislation lacks effective mechanisms to prevent abuses of basic human rights.
The ministry citied the problem of non-citizens in Estonia and Latvia, discrimination of Russian-speaking minorities in Finland and the rise of nationalist sentiments in Poland among examples of blatant human rights violations in the EU.
It also said UK authorities violated human rights while tapping conversations by its citizens and foreign delegations, citing revelations by US intelligence leaker Edward Snowden.
The ministry also criticized the 28-nation union for its "hypocritical” entry policies that violate the freedom of movement, citing a report by the Council of Europe Commissioner for Human Rights Nils Muiznieks.
"The European Union creates artificial obstacles for entry on its territory, which violate a person’s right for the freedom of movement and have a particularly negative impact on Roma people and asylum seekers,” the report reads.