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A seemingly unceasing series of glitches in the computer system of Mexico’s National Customs Agency (ANAM) disrupted freight movements in and out of the country for up to three days last week.

Worst affected were truck moves across the US border, but ports and airports also experienced problems.

According to ANAM, the glitches in the system occurred between last Tuesday and Thursday, but according to one source, they had begun on Monday. ANAM said it was struggling with problems affecting the agency’s ability to send out import and export declaration documents electronically, and informed users it was operating in “contingency” mode.

One commentator, however, described this as a euphemism, arguing that the system was essentially “dead” for two days.

On Thursday, ANAM announced that what it described as “intermittences” in its customs declaration validation system had been resolved, but some business organisations reported problems persisting.

In any case, the Federation of Mexican Customs Agents, which represents 99% of the nation’s customs agents, reported that many of the 50 customs offices were slow to respond to validation requests and, in some cases, such as Nueva Laredo and Queretaro, there was no connection.

The disruptions snarled truck traffic at border crossings, with the worst affected being Nuevo Laredo, where all freight operations were suspended at 10pm local time on Wednesday. International trade platform Aduanet advised users not to move cargo through Nueva Laredo until further notice.

Long delays for truckers were also reported at crossings at Ciudad Juarez and Tijuana.

International cargo flows at Mexico’s ports and airports were also affected, with delays of up to 48 hours. Ships were beginning to pile up at ports, as they could not offload their cargo, and yards were becoming congested.

The immediate fallout from the disruption has been heavy. The Mexican National Chamber of Cargo Transportation estimates the cost to be as high as $23m a day in lost revenue for the industry. It is unclear how much spoilage was caused to perishables shipments delayed at the border. The Mexican Meat Council warned that import delays could precipitate shortages for food production.

Glitches in the customs computer system are not a new phenomenon, but users said problems of this magnitude had not happened before.

And users are not happy about how the problem was handled. Fernando Ramos Casas, president of the Maritime Port Council, complained that until later on Wednesday there had been no statement from ANAM or the National Tax Agency, which had managed customs in the past and is still responsible for some of the duty agency’s systems. He got the impression, he added, that neither government agency was willing to take responsibility and resolve the problem.

So far there has been no indication what caused the problem, which leaves cargo owners and logistics providers wondering if there might be a possible repeat.

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