'TSA is experiencing significant, unprecedented technical issues with its computer server allowing the automated screening of checked bags for explosives,' TSA spokesman Nico Melendez said in a statement.

Melendez didn't elaborate on the problem, which began about 6:45am and only affected Sky Harbor. Around midnight, baggage screening was operational again, the airport announced in a tweet.

Earlier on Thursday, Melendez said it wasn't a safety issue.

'TSA is working diligently with our airline and airport partners and using alternative screening tools to screen bags, though that method are not as efficient as our automated system,' Melendez added. 

'TSA is currently bringing additional canine units from other airports and bringing in network specialists to address the situation and keep passengers safe and screen all bags.'

According to the TSA, the inline baggage systems handle the bulk of checked luggage. When everything is working properly only about 10 percent of all checked bags are hand-searched by TSA officers.