Trolleys not registered in the Container Centralen pool, of which the company estimates there are around one million, can be registered for £10.
The move comes ahead of the radio frequency identification (RFID) tagging operation to be introduced next year in an attempt to rid the pool of fake trolleys.
Container Centralen chief executive Tonny Vangsgaard Gravesen said the operation was now underway and progressing well.
"The amnesty period is now in force so if customers have more or fewer Container Centralen containers than on contract, they can contact the local office to get it corrected," he explained.
"We are having a lot of meetings with customers, customer groups and associations," he added. "Communication is really the issue for us at the moment because the technical side is ready. We have installed scanners at all our 58 depots across Europe and they are now in use to register all transfer data, but not yet for scanning."
The operations start date was postponed from November to January to give "customers more time to prepare and buy the scanners", according to Gravesen. The scanners needed to read the RFID labels cost £300.