The 25-year-old had been hoping to enjoy an injury-free pre-season, allowing him to start the 2014/15 campaign at peak fitness.
Having spent much of last season on the treatment table as he nursed his way back from a serious heel complaint, the last thing he wanted was to suffer a fresh setback.
West Ham hope the problem is not too serious and plan to rest Carroll as a precaution.
They remain confident that the England international will be ready for the start of the new Premier League season and that there will be no repeat of the concerns from 12 months ago.
A statement posted on the club’s official website read: "After assessment by the Club's medical experts, it was decided to let the England international rest for both remaining games and receive intensive treatment to ensure he is fit for the start of the season.
"It should be clear that the affected area is not in any way associated with the previous injury he successfully overcame towards the end of last season."
West Ham are due to face Wellington Phoenix in Auckland on Wednesday morning before travelling to Wellington to play Sydney FC on Saturday.