A pontoon at the newly-launched Mtongwe ferry channel was on Wednesday swept away by Indian Ocean waves.
This disrupted services at the channel reopened by President Uhuru Kenyatta and DP William Ruto in February.
The channel's relaunch escalated the political differences between the President and Governor Hassan Joho.
Joho was barred by GSU officers as he attempted to join the national government leaders at the event.
Uhuru, at that time, asked Joho to focus on Mombasa issues instead of following him around.
The pontoon is said to have been carried away after its two pillars were swept by heavy tides.
"No one was injured during the midnight incident," Bakari Gowa, Kenya Ferry Services managing director, said.
"At the moment, operations at the mainland will proceed but the Bandari side will remain closed for few days."
Gowa said the users have been redirected to land at the Likoni crossing channel.
"We know it will inconvenience people. We will be ferrying commuters from the Mtongwe channel to Likoni."
A trip between the two points, 3kms apart, will now take at least 30 minutes.
The channel had been closed after its two ferries were decommissioned in 2012.
"KFS has already deployed a team of engineers to work on the damaged pontoon so that operations resume," Gowa said.
He said the engineers, working with their counterparts from the Transport ministry, will also assist in rebuilding the pontoons.
Gowa said the company is considering constructing landing ramps to avert such disruptions in future.
"KFS does not have adequate land for the construction. We are sourcing the extra space from residents who are willing to sell their land."
“We have Sh120 million for building ramps. If we get land, it will only take four months to have them operational," Gowa said.