The band had been expected to play the Bournemouth Air Festival on Friday evening as part of a four-night event.
However, organisers cancelled the final part of Friday’s show when “unprecedented” high levels of water reached the beach.
A statement on the festival’s Facebook page said: “Unfortunately a combination of exceptional wind and sea conditions, that could not be fully anticipated, have resulted in the cancellation of tonight’s final part of the show.
“This was caused by direct southerly/south westerly winds and short period strong waves which added to the forecast high spring tide.
“This created high levels of water on the beach that had been unprecedented in all the years of staging the event.
“This decision was taken in the interest of public safety and the organisers are grateful for the co-operation and understanding of everyone involved.”
Kaiser Chiefs posted a video message on Twitter in which they apologised to fans and said “some things you can’t predict”.
Lead singer Ricky Wilson said: “Tonight our show in Bournemouth was cancelled - the stage was in danger and they didn’t want it falling on you, and they didn’t want us on it when it fell. Sorry we didn’t go the gig, we will be back in February.”
Organisers said the high water levels had damaged the beach stages and more severe storm conditions were forecast for Saturday.
A statement said: “The decision has been taken to cancel the ticketed Sunsets on the Beach at Boscombe Pier and the evening entertainment on the stage at Bournemouth in the interests of public safety.
“As a result of this advance cancellation, ticket holders will be contacted in the next few days once the insurance company has been consulted.”