Spain's attempts to end the closed shop system that dominates ports and harbours - as it does in major North American ports - have been met with crippling dock strikes with more planned for later this month.
While the court said Spain showed "goodwill in cooperating" with the investigation, Madrid still failed to deregulate stevedoring in Spanish ports 29 months after being so ordered.
The EU first urged Spain to deregulate in December of 2014, stating the nation was failing to comply with European stowage rules.
The European Commission called for a fine of EUR134,107 a day that Spain neglected to deregulate the ports, but the courts settled on a fine of EUR27,552 per day covering 108 days.
Madrid passed a new law on port stowage services, which aroused more labour obstruction, causing the imposition of the fine to be delayed.
The European Commission has also referred Spain to the court again for failure to implement EU rules on whistle-blowers. The 2014 rule on whistle-blowers is in response to infringements of the Market Abuse Regulation and requires nations to protect whistle-blowers and personal data.