Analysts polled by Dow Jones Newswires had forecast a June decrease of just 0.3 percent.
On an annual basis, retail sales in the biggest European economy gained 3.1 percent, in large part because there was one more shopping day this year than last, the Destatis data showed.
German shoppers were thus still holding back even as the economy surged out of its worst postwar recession thanks to strong performances by exporters.
Third quarter results released so far have underscored robust earnings in the auto, chemical and public works sectors.
Consumer sentiment has improved and unemployment could fall further, but the stores are not really seeing any benefit so far.
"Despite the surprisingly favourable labour market development, private consumption is not picking up," Commerzbank economist Ralph Solveen said.
In the first six months of the year, retail sales slipped by 0.4 percent from their level in the same period of 2009.
The medium-term measure is considered more reliable than monthly data, which are often revised later on.
A provisional monthly rise of 0.4 in May was revised sharply higher on Friday to a gain of 3.0 percent, for example.