Remaining services to and from Heysham were expected to sail but with some delays.
BBC: Isle of Man ferry collision: Ben-my-Chree back in service
The ferry was docking from Heysham when it hit the fender at about 17:45 BST on Wednesday.
BBC: Isle of Man ferry collision: Ben-my-Chree back in service
Heysham Moss is a peat bog which is home to a wide range of plants and animals.
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The truck ferry was travelling from Warrenpoint in Northern Ireland to Heysham, Lancashire, when she ran into difficulty just before 2000 GMT.
All Friday's sailings to Heysham and Liverpool have been cancelled, while Saturday's 02:15 GMT ferry from Heysham to Douglas is also not operating.
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Heysham Moss supports a number of bog plants including round leaved sundew, bog myrtle, bog rosemary, bog asphodel and the locally-rare white beaked sedge.
Chief Executive Mark Woodward said: 'We managed to effect the temporary repairs sooner than expected, which enabled her to operate a freight-only service to Heysham this morning.
BBC: Isle of Man ferry collision: Ben-my-Chree back in service
The repaired ferry sailed freight to Heysham at 10:00 BST.
BBC: Isle of Man ferry collision: Ben-my-Chree back in service
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