Iona, a P&O Cruises ship, had its departure from Southampton delayed from Saturday until Sunday as a result of the debris.
The cruise ship, which has a capacity of 5,200 passengers, eventually set sail at 1pm on Sunday for a 14-day trip to Spain, Portugal and the Canary Islands.
An MCA spokesman said: “HM Coastguard is continuing to work with the relevant authorities after 16 containers went overboard from the cargo ship Baltic Klipper in the Solent on 6 December.
“This includes working with the vessel’s owners, who are responsible for recovering the containers. Eight of the containers were reported as carrying bananas, two as carrying plantain, one as carrying avocados, and the remaining five as empty.
“Two containers have come ashore at Selsey, where a cordon has been put in place. Coastguard rescue teams from Selsey and Littlehampton, West Sussex Fire and Rescue Service and Sussex Police are all in attendance.”
