The incident appears to be a "malicious attack designed to strain our operation and bring our systems to a halt," she said in a statement.
Telephone booking, online booking and online timetable services have all been affected.
"We are still in the midst of resolving the situation - data theft does not appear to be a motive.
We prioritized our investigation to check for any evidence of personal data leaks and can confirm that we have not found any evidence to suggest that any such leaks may have occurred," Collins said.
As customer credit card data is not held on the company's IT systems, the firm says there is no risk of card number theft. Red Funnel connects Southampton with the Isle of Wight with 35 sailings a day, including a high-speed foot passenger ferry service and a ro/pax vehicle ferry service.
The attack is the latest in a rash of cyber incidents affecting maritime stakeholders.
CMA CGM reported a major cyberattack earlier this week, and it has not ruled out the possibility of a data breach.
The International Maritime Organization has also sustained a cyberattack taking its public-facing website offline, IMO reported Thursday.