The difference in average hourly pay between German men and women fell by just 1.2 percentage points between 2008 and 2013, the figures show.
That made Germany the fourth-worst country for female employees in the EU, behind Estonia, Austria and the Czech Republic.
The news will give fresh ammunition to Families Minister Manuela Schwesig, who hopes to introduce a wage transparency law which would allow women to check their salary against those of men doing similar work.
While the gap shrank in most EU countries, there were increases in nine member states, with Eurostat pointing out particularly large increases in Portugal, Spain, Latvia, Italy and Estonia.
The statisticians also looked into full- and part-time work among women, finding that states where women could work part-time had higher overall female employment rates.
This was true of Germany, but also Sweden, Denmark, the Netherlands and Austria.
Exceptions to the trend were Finland and Estonia, where much larger numbers of women were working full-time.
But women were much less likely than men to be employed as managers across Europe.
In Germany, just 29 percent of managers are women compared with 49 percent of the total workforce.
The country was well behind leaders Hungary, Latvia and Poland.