The decision takes into account the significant costs involved to implement the technology and lack of supporting facilities at foreign ports to enable such screening for radiological materials and nuclear weapons.
The implementation deadline had already been delayed from 2012 to July 1, 2014.
In a letter earlier this month to Thomas Carper, chairman of the Senate Committee on Homeland Security and Governmental Affairs, Mr Johnson said that the use of systems available to scan containers "would have a negative impact on trade capacity and the flow of cargo."
He said scanners to monitor the 12-metre containers imported into the US each year "cannot be purchased, deployed or operated at ports overseas because ports do not have the physical characteristics to install such a system."
The letter, seen by Lloyd's List, also draws attention to the huge cost of such a scheme. "I have personally reviewed our current port security and DHS' short-term and long-term ability to comply with 100 per cent scanning requirement," he writes.
"Following this review, I must report, in all candour, that DHS's ability to fully comply with this unfunded mandate of 100 per cent scanning, even in the long term, is highly improbable, hugely expensive and, in our judgment, not the best use of taxpayer resources to meet this country's port security and homeland-security needs."
The Department of Homeland Security (DHS) will instead aim to increase the percentage of containers scanned abroad, with the emphasis on high-risk cargo, thought to represent less than one per cent of US-bound containerised cargo.