Ferry moved into the water as refit nears completion
It added the "out of water" inspections showed further essential work was required, which increased the time in the dock.
The next stage of the work could only be completed with the vessel in the water, resulting in Lynher being moved to a berth alongside the dock.
While in the dry dock Lynher was repainted both above and below the waterline.
Tamar Crossings said dry docking allowed inspections to be carried out by its team and regulators to ensure that the vessel would be safe for a further five years.
Initial works also took place to replace the outdated computer control system, it said.
The new control system, supplied by Rolls Royce, would need to be integrated with the ferry's existing equipment.
Tamar Crossings
Tamar Crossings added that the next stage of the complex work could only be completed with the vessel in the water.
It said work on this phase was scheduled to begin on Thursday and would take two weeks to complete.
It would then need to pass the Harbour Acceptance Testing before it could return to Torpoint.
Lynher is expected to return to Torpoint in the middle of June, depending on weather and sea conditions, Tamar Crossings said.
It added that a combination of bad weather at the start of the refit process and the impact of carrying out additional vital repairs meant Lynhers return to the water was later than originally planned.
The service will continue being provided by the two remaining ferries, one leaving each side of the river every 15 minutes between 06:30 and 22:00 BST.
There will also be a single half-hourly night service ferry from 22:00 to 06:30.
