Rutte was to have inaugurated the scanner on the frontier with the Palestinian Islamist-ruled enclave, but the ceremony was put off because of the row.
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"Installation of the Dutch scanner, which would have been used to verify the contents of containers from Gaza destined for export, was postponed after the Netherlands made unexpected demands," the official told AFP, speaking on condition of anonymity.
"Technically, there is no problem about the scanner at the Kerem Shalom crossing through which goods originating in Gaza pass," the official said.
"But the Dutch suddenly imposed political conditions, notably on the percentage of merchandise destined for the West Bank or abroad.
"These are political issues that need to be resolved at the highest level, which will delay the start-up of the scanner."
Media reports said the row meant the ceremony at the crossing originally due for Sunday, with Rutte present, was cancelled.
The focus of the dispute is exports from Gaza to the West Bank, which is controlled by the Palestinian Authority under president Mahmoud Abbas .
Despite attempts by Egypt, Israel and some in the PA to isolate the two Palestinian regions, the Dutch officials had hoped the scanner might boost commerce between them, the media reports said.
After Gilad Shalit was captured in 2006 by Gaza-based terrorists, a blockade was imposed on the Palestinian enclave.
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