The developer has told BBC News the gaps are not a concern and all artificial reefs built with similar construction techniques have similar gaps.
An ASR spokeswoman said: "The reef is not for inexperienced surfers and there is an inherent risk related to surfing, whether surfing on artificial, or natural, reefs."
The surf reef is predicted to bring £10m into Bournemouth every year
The council said all safety issues will be resolved before the reef is opened, adding final construction work is still taking place.
"We are very close to being able to sign off the project as complete - and of course this includes having completed all health and safety checks to our satisfaction, a spokeswoman said.
She added RNLI teams would pay particular attention to sea conditions on and around the reef, as well as the competency of the surfers.
"Beginners can take lessons and learn to surf with a school," she said.
"When surfers are competent, they can then progress on to the surf reef.
"Our signage on site will make this very clear."
We have to stress to you that the reef doesn't actually create new waves, but helps control where the existing waves break
The e-mails also reveal that in June, the council was trying to get answers from ASR about the expected performance of the reef.
Both ASR and the council now say performance will be judged on the quality and shape of the waves, and the number of "surfable" days compared to previous years.
Plymouth University will monitor the reef for 12 months after its completion, to study how it fares.
The council is waiting for the reef to produce results before it is launched, the e-mails show.
"Otherwise, the media will come down and see the sea is flat and report that the reef isn't working and we could have a widespread negative story on our hands," a member of the council communications team said.
But ASR responded by saying the winter months were typically the best for surfing conditions.
"We have to stress to you that the reef doesn't actually create new waves, but helps control where the existing waves break," the spokeswoman said.
"So if the ocean is calm and flat, this does not mean that the reef is not working."
She added the reef would also help to create a new marine ecosystem and had been a catalyst for "huge socio-economic benefits in Boscombe".
The reef is part of an £11m ongoing regeneration of Boscombe's seafront which the council hopes will boost the economy by £3m a year and attract up to 10,000 surfers.
It will be one of a number of similar artificial reefs of its type worldwide, built by ASR including developments in Narrowneck, Queensland, and Mount Maunganui, New Zealand.
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