The agency moved as ministers published a damning l report into the grounding of the supertanker at the entrance to the Welsh port and the six-day salvage operation which followed.
The agency has charged Milford Haven Port Authority and harbour master Clive Andrews with committing pollution offences under common law and the Water Resources Act 1991.
Last night the port authority said the charges were ``misconceived''.
The Liberian-registered tanker lost nearly 72,000 tonnes of crude oil, over half its cargo, when much of its bottom plates were holed or scraped off in February 1996. It was Britain's worst oil pollution disaster since the Tory Canyon 30 years ago.
Fishing grounds were closed and more than 100 miles of coastline - much of it in Britain's only coastal national park - was heavily slicked. Thousands of seabirds were killed. The report by the Government's Marine Accident Investigation Branch makes dozens of serious criticisms of the port, the Government's Marine Pollution Control Unit and the consortium of private enterprise salvors - and 24 recommendations.
``The immediate cause...was pilot error,'' says the report. Pilot John Pearn failed to keep the huge ship in the deepest part of the Channel. The ship's Russian captain, Eduard Bognov, was also blamed for failing to appreciate where the pilot was going wrong, and failing to know his intentions.
``The pilot's error was due in part to inadequate training and experience,'' says the report. Examination and training standards for the port's pilots were unsatisfactory, and there was a ``deep rift" between them and the authority. Mr Pearn still works as a pilot at Milford Haven. He was demoted to handling smaller vessels after a disciplinary hearing, but reinstated after an appeal.
After the initial grounding the salvors and authorities decided to use tugs to hold the damaged, listing ship in a small area of deep water at the harbour entrance. The plan was to pump the oil into another tanker; the Sea Empress would then have been floating high enough to bring her into port without grounding.
But two days later, as a gale blew up, the salvors decided to turn the supertanker to face the wind and waves. The tugs lost control; the strength of a tidal stream had been misjudged.
The Sea Empress was then swept onto rocks suffering much worse damage. It was another four days before the tanker was finally floated off and reached the harbour.
The accident report cites communication and management failures and missed opportunities during the operation. But, it says, the most important factor in the escalating pollution disaster was the lack of understanding of the strong tidal currents at the entrance to Milford Haven.
Marine Pollution Control Unit staff at the scene were undermanned and overstretched, and key members were sometimes diverted from their primary job to brief the media. The unit's overall commander, Chris Harris, should have gone to Milford Haven sooner rather than remaining at Southampton headquarters, said the report.
Deputy Prime Minister John Prescott said the Pilotage Act, which covers standards and training for pilots, would be reviewed and Lord Donaldson, would also carry out a review of the command and control of salvage operations.