Ivan Krastev said countries such as Romania, Bulgaria and the Czech Republic enjoyed a brief honeymoon period after joining the EU but now feel like they have been taken advantage of.
The Eastern Europe expert said Mrs Merkel had “suddenly changed the rules” during the 2015 migrant crisis, a decision which led to poorer nations in the east being forced to take their share of new arrivals.
And he warned the EU’s failure to agree a long-term solution to rehoming refugees and asylum seekers was only making the situation worse.
In an interview with German newspaper Welt am Sonntag, Mr Krastev said: “The Eastern Europeans are now feeling like the biggest losers.”
In 2015, the EU saw a huge spike in the number of people applying for asylum as hundreds of thousands of people arrived after fleeing conflict in the Middle East and Africa.
In response to the increase, Mrs Merkel agreed to accept more than one million refugees into Germany.
After more than one million more people applied for asylum in 2016, Brussels warned Eastern European counties they would be stripped of EU funding if they refused to take their fair share of arrivals under the bloc’s controversial quota system.
EU Commission President Jean-Claude Juncker told the former communist counties that the “solidarity” shown by the EU was not a “one way street”.
The plan was fiercely opposed by countries like Poland, Slovakia and Hungary but its implementation has only served to spread discontent in the former soviet republics, Mr Krastev warned.
He said: “We were asked to accept a relatively small number and to show solidarity after having experienced solidarity ourselves.
“The refugee crisis is causing a massive dispute between Western and Eastern Europe.”
Mr Krastev added Mrs Merkel had become a symbol of an EU which has become an enemy in the eyes of many Eastern Europeans.
He said her controversial decision on the migrant crisis had led to a change in the bloc’s policy, and ultimately resulted in poorer nations being forced to accept refugees or risk losing out on much-needed funding.
He added: ”During the euro crisis, Germany had made everyone commit to keeping the rules if they wanted to preserve Europe
“Now it suddenly changed the rules.”
(Additional reporting by Monika Pallenberg.)