Politicians said the clip, '1989-2009: 20 years of liberty', produced by the European Commission, focused too much on Germany without mentioning the achievements of Poland, the EU's biggest ex-communist country.
Poland's ambassador to the EU, Jan Tombinski, said the clip could sour the public mood towards the EU ahead of the European Parliament elections in June.
On Monday, Tombinski wrote to the EU's communication policy chief Margot Wallström to demand changes in the clip, available on the Commission's website.
"The simplistic vision presented in the clip may instead introduce needless controversies which should be avoided during the European elections campaign," the letter said.
The clip is part of an EU campaign to commemorate the 20th anniversary of the fall of communism in central and eastern Europe, where most countries now belong to the EU.
Analysts say the debate on the clip could give ammunition to Eurosceptics in the campaign to the European election against pro-EU, right-centre government of Prime Minister Donald Tusk.
The Commission rejected the criticism, although it promised it would correct one inaccuracy in the clip.
"It is quite an artistic video clip. This is not a historical programme, this is not a documentary," a Commission spokesman said.
Some historians and sociologists say the Poles are especially sensitive about their history because it was so tragic - the country has often been dominated by foreign powers and staged many bloody, unsuccessful uprisings. Polish politicians are bitter that the clip, depicting moments from a life of a boy born in 1989, focuses on the Fall of the Berlin wall while ignoring earlier round-table talks in Poland, the creation of the first non-communist government there or the anti-communist Solidarity trade union.
The Poles criticised their country being represented in the clip only by the communist strongman, General Wojciech Jaruzelski, rather than by late Polish-born Pope John Paul II, who helped inspire opposition towards communism.
(EurActiv with Reuters.)