A group of small parties had asked the Karlsruhe-based constitutional court to review Germany's existing 3% threshold, saying it was unfair and put off potential supporters.
Polls have suggested small groups including eurosceptic Alternative for Germany (AfD) could do well in the European elections and potentially disrupt mainstream political blocs.
AfD already has 4-5% support, according to surveys. But other parties that could benefit without the hurdle include the anti-establishment Pirates, Free Voters and the Ecological Democratic Party.
Germany's mainstream parties have long argued electoral thresholds are needed to avoid political fragmentation in parliament of the like that helped bring down the Weimar Republic and made way for the rise of Adolf Hitler.
But the constitutional court already ruled in 2011 that the then 5% threshold was void, saying there were not sufficient grounds to justify "the serious interference with equal suffrage and equal opportunities of political parties".
Berlin only reduced the threshold to 3% last year.