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Companies that thought they were well prepared for potential disasters were thrown into turmoil, when the attacks revealed holes in their planning, risk consultant group Kroll said last week.
Firms with long-established contracts with specialist disaster recovery centres ran into problems as the scale of the tragedy left disaster recovery suppliers overwhelmed.
"Companies had contracts but there was no room left at the disaster recovery centre. They didn't realise it was first-come, first-served," said Alan Brill, senior managing director at Kroll.
"While people were thinking about whether to make the call to invoke a plan that would cost $20,000-$30,000 [£13,300-£20,000], other people were signing the contracts and getting in," he added.
One company ran into difficulties because it kept all the copies of its emergency back-up plan in its office in the World Trade Center. When asked why, the company said the plan was too confidential to be let out of the building, said Brill.
Another company had chosen to put its IT centre in one tower and an emergency back-up centre in the other tower.
Even firms that escaped tower attacks ran into unexpected difficulties, said Brill speaking at the Compsec security conference. "Businesses forgot that there would be an exclusion zone," he said.
Financial services companies affected by the destruction of the World Trade Center will have to spend $3.3bn to rebuild their software and hardware systems, according to financial services analyst firm TowerGroup.
Additional reporting by Emma Nash, CW360.com