Government sources told daily Rheinische Post on Thursday that the security checks took place across the country on Wednesday, but were focussed mainly in the populous state of North Rhine-Westphalia.
In the coming weeks some 650 such companies will undergo similar examination, the paper said.
Five logistics and shipping companies in North Rhine-Westphalia were checked, including the freight centre at the Cologne-Bonn airport.
No major security violations or problems were found, but several of the X-ray machines did not meet technical regulations, the paper said.
“Here an immediate technical overhaul was ordered,” the report said.
German Transportation Peter Ramsauer said he wanted to put tougher controls in place for mail services provided by airlines.
“We must make the links of the delivery chain more secure,” he told the paper, adding that companies should expect “unannounced checks at any time.”
Last week German authorities banned all flights from Yemen in reaction to parcel bombs posted in the country that were found on US-bound cargo flights. One of the packages - allegedly connected to an al-Qaida plot - had passed through the Cologne airport over the weekend without being stopped until it was discovered in Britain.
Then security officials seized and disarmed an explosive package delivered to the Chancellery in Berlin on November 2. The package was intercepted the same day similar parcel bombs exploded at the Swiss and Russian embassies in Athens in a wave of attacks linked to leftist extremists in Greece.
The next day, Chancellor Angela Merkel demanded better international coordination on security measures for cargo and postal services, calling on the world to remain vigilant against terrorism.
Over the weekend the government said it was considering a "black list" for airports around the world that do not meet security standards.