McCullum had a scan "and the decision is that he return to New Zealand immediately for further review and to begin rehabilitation," New Zealand Cricket said in a statement.
He was initially scheduled to fly home after the Bangladesh tour, missing the subsequent limited-overs series in Sri Lanka.
But team physiotherapist Paul Close said: "Brendon's back needs careful management. It's flared up and is giving him significant pain. The best course of action is getting him home for rehabilitation as soon as possible."
New Zealand drew both Test matches against lowly Bangladesh and lost the first two ODIs.
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