It had been decided that Harmison would return early after playing in the final four-day match in Australia to enable him to rest before Durham's tour to South Africa next month.
"He started the game but partially dislocated his shoulder," said Durham's Director of Cricket Geoff Cook.
"We won't know how serious it is until he gets home within the next few days.
"We have been told that he has done OK, although his runs per over are still a slight concern. Rodney Marsh is coming over in April to spend the summer here and monitor the Academy boys' progress and act as a sounding board for the England selectors.
"Duncan Fletcher is very keen on Harmison and will take any chance to have him involved."
Harmison was said to be on stand-by for the Test matches in New Zealand in case Jimmy Ormond failed to recover from an operation.
But this latest injury is likely to add to the impression that he needs a rest.
Durham all-rounder Gordon Muchall, a newcomer to the full-time staff, has stayed on in Perth with clubmates Nicky Hatch and Gary Pratt after completing his Under 19 World Cup duties.
Others completing stints overseas are Jimmy Daley in Cape Town and Chris Mann in Melbourne, while spinners Graeme Bridge and Nicky Phillips are leaving shortly for Adelaide, where they will work for two weeks with former Australia off-spinner Ashley Mallett.
Seamer Mark Davies, whose season was ended by a collapsed lung last September, had an operation in December and is now fully fit, as are Simon Brown and Neil Killeen.
Both missed most of last season through injury.
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