Somalia has overtaken Iraq as the world's most dangerous country for minority groups
Sudan, Afghanistan and Burma followed in the global survey by the Minority Rights Group International (MRG).
It alleges the US ignored abuses of minorities in countries supporting the US "war on terror" including Pakistan, Turkey and Israel.
Sri Lanka saw the highest rise in persecutions with renewed fighting between government and rebel forces.
"A new government in Somalia has raised hopes for democracy, but it is also a uniquely dangerous time," said MRG's director Mark Lattimer.
"There is the spectre of a return of large-scale clan violence - and groups that supported the old order are now under tremendous threat."
MRG said the Darood, Hawiye and Issaq clans are under threat as well as the Bantu group.
Sudan is the third worst offender, said the State of the World's Minorities report, because of the violence in Darfur.
More than two million people have been displaced since the fighting began in 2003 and the UN says refugee camps in the region are almost full.
At least 200,000 have died in the ongoing violence between pro-government Arab Janjaweed militia groups and rebel groups in Darfur.
The MRG said farmers from the Zahgawa, Masalit and Fur groups, amongst others, have been targeted.
Minority groups in Iraq including Christians, Yezidis and Mandaeans face targeted killings, abductions and torture.
The group's study links tensions in Turkey surrounding the EU accession process to a surge in religious and nationalist extremism behind attacks on minorities - such as the murder of Turkish-Armenian writer Hrant Dink at the end of 2006.
"US allies have managed to barter their support for the war on terror in return for having their human rights records ignored," said Mr Lattimer.
The MRG also blames the "war on terror" for a rise in anti-Muslim attacks and intimidation within the European Union affecting millions of ethnic Arabs, South Asians and other Muslim minorities.
In Sri Lanka, minority Tamils and Muslims are caught up in fighting and increasingly becoming targets for abduction and disappearance after the breakdown of peace efforts between Tamil Tiger rebels and government forces last year.
"In three-quarters of the world's conflicts, the killing is now targeted at particular ethnic or religious groups," said Mr Lattimer.
"Because they are usually minorities their suffering is largely ignored."
Minorities in Pakistan are not safe: report