The Red Funnel service from Southampton was travelling through dense fog as it approached the Isle of Wight at about 8.00am on Sunday.
HM Coastguard received a 999 call from a member of the public shortly after, who reported hearing cries from within the harbour.
A RNLI spokesman said three lifeboats looked for people in the water off the coast of Cowes in the aftermath of the accident.
The Maritime and Coastguard Agency later said in a tweet: “HM Coastguard can confirm that nobody is in the water or missing in Cowes Harbour.
“We made contact with the person who was heard crying for help and he is safe and well.
“He was on board his own vessel and calling out to try and alert the master of the ferry #allsafe.”
Red Funnel said the ferry, named Red Falcon, is watertight and no injuries were sustained by the 40 passengers onboard.
The lifeboats have now turned to the shore and the rescue operation is over.
A tug boat has pulled the ferry off the pud and back to its usual berth.
The Red Falcon’s passengers and crew have disembarked.
Cowes Harbour is currently closed to traffic.