The recording, made at a Greenpeace staff meeting earlier this year, was leaked along with other material to The Guardian, which yesterday reported financial problems at the organisation.
Naidoo said: "… Let me just concede that we have a huge problem with the way we are doing communications. I want to own that and take responsibility for that. It’s not where it needs to be."
"There’s good reason why people actually are upset about a range of things. But when I looked at what the problem was, it was actually a patent lack of communication, not just a lack of communication but not communicating at the right time, and things not clear," he added.
According to The Guardian, several Greenpeace staff were unhappy amid a major restructure involving moving people out of its head office in Amsterdam to national offices around the world. Greenpeace has also had problems in its financial department, which it transpired earlier this month had lost £3m on the foreign exchange market.
Greenpeace released a statement last week stating that the losses were a result of "a serious error of judgement" by an employee in its financial department who had not been given authorisation to buy foreign currency.
Following the report yesterday, Naidoo said a new global finance director, Chris Fyfe, was beginning to make changes within the department.
He said: "We’re funded entirely by the public so we can retain complete independence, and keep faith with our values. That’s why we have to retain the trust of the public, and that’s what the changes I’ve made are going to do."
He added: "This restructuring is not about reducing the number of people working full time on Greenpeace campaigns. It’s about making sure we have people where we need them, and increasingly that’s not in Amsterdam."