Eastern member countries have complained bitterly of "food apartheid" or being treated as "Europe's garbage can" by manufacturers who they say cut corners on the ingredients used in a whole range of everyday goods.
Critics and the companies say the claims are unfounded, reflecting different tastes not contents, but Juncker insisted the problem was real and must be tackled.
"I don't like the idea that there would be some kind of second category citizens in Europe," Juncker said after talks in Brussels with Slovak Prime Minister Robert Fico.
"This is totally unacceptable."
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Fico, who last week described the issue as an "international scandal," said he welcomed Juncker's commitment to solving the problem.
"The most important fact for me is that the Commission and the president accept that the problem exists and that the president has pledged to devote attention to this issue," Fico said.
"It might seem ridiculous to some people" but for Slovakia and its Visegrad 4 partners -- the Czech Republic, Hungary and Poland -- it was "a serious political problem," he said.
Government-backed studies in Hungary, Slovakia and the Czech Republic appear to show that many items sold with identical packaging were of superior quality in other EU countries.
Bulgaria said earlier this month that its research showed discrepancies in at least seven out of 31 products bought from the same chain stores in Germany and Austria.
Under EU directives, companies are free to change a product's ingredients from one member state to another as long as they are clearly listed on the packaging.
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