German police entered the cockpit and found the 40-year-old in a "highly intoxicated condition" on Friday evening, a statement said.
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An airport official had sounded the alert after finding the pilot "reeking of alcohol and walking unsteadily," it said.
Stuttgart prosecutors immediately suspended the co-pilot's flying licence and fixed a $12,000 bail.
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Portugalia cancelled a flight from Stuttgart to Lisbon on Friday night with 106 passengers.
TAP said it would "open an enquiry and take necessary measures" and apologised to passengers for the inconvenience caused.
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