Skipper Stephen Humphreys, 33, from Greenock, deckhand Eric Blackley, 57, of Gourock, and their colleague Robert Cameron, 65, died on 19 December 2007 when the Greenock-based tugboat sank at Clydebank.
As the fifth anniversary of the Flying Phantom tragedy approaches the Telegraph can today reveal that proceedings against both Clydeport and vessel operator Svitzer have been raised under the Health and Safety at Work Act 1974.
A spokeswoman for the Crown Office said: "The families of the three men who died are being kept advised of significant developments.
"Criminal proceedings were raised against two companies in relation to the sinking of the Flying Phantom which resulted in the loss of three crew members."
The sinking of the Flying Phantom back in 2007 shocked the people of Inverclyde and hundreds of mourners turned out at the funerals of the two local victims.
A book of condolence was also opened.
Only one member of the crew, 37-year-old Brian Aitchison, from the Borders, survived the accident.
Following the publication of a report by the Marine Accident Investigation Branch three years ago the heartbroken families of the men went public with plans to launch a civil action against the two companies.
They also called for a Fatal Accident Inquiry into the circumstances surrounding the sinking of the Phantom.
Tugboat operators Svitzer, who have a base in Greenock, today said they did not want to comment on the criminal proceedings.
But a spokesman said: "Our thoughts are with the families of all three men who died in the tragedy, especially at this time."
When contacted by the Tele the port authority Clydeport did not wish to make any comment.
Criminal proceedings against the two companies have been raised at Dumbarton Sheriff Court and so far no further court dates have been set.