"Thousands of refugees, asylum-seekers and migrants -- including children -- making dangerous journeys across the Balkans are suffering violent abuse and extortion at the hands of the authorities and criminal gangs," the rights group said in a report.
Migrants fleeing war, poverty and persecution were being "shamefully let down by a failing EU asylum and migration system which leaves them trapped without protection in Serbia and Macedonia," the London-based group said.
The number of migrants and refugees from Syria, Afghanistan, Egypt, Eritrea, Iraq, Nigeria, Somalia, Sudan and Tunisia, travelling overland through the Balkans on their way to EU, has dramatically increased in recent years.
The number of people apprehended crossing the Serbia-Hungary border alone has risen by more than 2,500 percent since 2010 -- from 2,370 to 60,602, Amnesty said.
The journey takes them by sea from Turkey to Greece and then overland across Macedonia and Serbia towards EU-member Hungary, a route that is increasingly used as it is considered less deadly than sailing across the Mediterranean from Libya.
More than 1,800 people have been killed attempting to cross the Mediterranean this year alone, according to the United Nations.
Amnesty's report is based on four research missions to Serbia, Hungary, Greece and Macedonia between July 2014 and March 2015 and interviews with more than 100 refugees and migrants, AFP reported.
Gauri van Gulik, Amnesty's Deputy Director for Europe and Central Asia, said that Serbia and Macedonia had become "a sink for the overflow of refugees and migrants that nobody in the EU seems willing to receive".
Many migrants told the rights group that they have been forced to pay bribes of up to 100 euros ($110) to police while passing through the Balkans.
Last month Serbian police arrested 29 police officers and nine customs officials suspected of corruption and abuse of power, accusing them of taking bribes to let migrants illegally pass through the border to Hungary.