Planes were grounded for hours at the southeastern regional airport which normally takes passengers to 30 international destinations.
Earlier passengers were taken to other airports by bus amid chaotic scenes, the ANP national news agency reported.
"The first plane of today has just departed," Eindhoven Airport said on its website, but it advised passengers to continue to check flight schedules.
The country's main airport, Schiphol near Amsterdam, which is a major European hub, was unaffected.
Meanwhile the Dutch defence ministry -- which had been blamed as the source of the online disruption -- said systems hit were slowly being restarted, warning it would take several hours.
"We have pinned the cause and will give more information once we have the full picture," the ministry said on X, formerly Twitter.
"Currently there is no indication that this was an act with malicious intent," it added.
The outage also hit other public services in the Netherlands.
The coastguard said in an earlier statement it was "not reachable" due to the outage, either by telephone or radio. It urged people in an emergency situation to call the 112 emergency number.
The contact centre of the military police was also not reachable, authorities said. It was also not possible to make an appointment for a Covid vaccine.
Last month, airlines, banks, and media worldwide were thrown into chaos by one of the biggest IT crashes in recent years, caused by an update to an anti-virus programme.
ric-jhe/imm
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