Mr Huebner wrote that he was not talking about people assigned to positions that required them "to stretch a bit", but people who "exhibit no understanding of management processes, dynamics, or requirements being put into positions of authority, and who thus affirmatively disrupt the operation of the Missions and harm American interests".
"I do not make that last statement lightly," Mr Huebner wrote, adding that when he arrived in his post in late 2009, half of senior officers in Wellington and Apia weren't performing to acceptable standards.
That created serious morale, retention and performance issues for junior staff members, and "after six months of remedial mentoring and engagement, I prepared to curtail the three most destructive officers".
Mr Huebner - who wrote that he had "a laser focus on mentoring and skills building" - said he then took an active role in recruitment, thinking that would solve the problem which he attributed to New Zealand and Samoa attracting a disproportionate share of "lifestyle" or "problem" officers, "because the posts have for the past two decades been low-activity, low-ambition outposts".
However, at the time of writing the 2012 email, he found that many incoming staff members also had poor management skills.
"I would hope that my observations are not unduly discounted because I am a political appointee," Mr Huebner wrote. "I have been particularly impressed with the resilience, ambition, and focus of my junior officers and many of the local staff.
"I am, however, deeply concerned with the serious - and inexplicable - skills deficits that we continue to encounter at the upper-mid and senior levels. I am raising the issue again now because certain of my 'new' officers share the dysfunctions of the legacy officers when I arrived, and I fear that the significant advances made at Missions in New Zealand and Samoa - and consequently in our bilateral relations with those two nations - may and likely will evaporate under a less-hands-on or more culturally-casual COM."
Mr Huebner asked if a management trainer could be sent out for a week of intensive remedial training.
In an earlier August 16 email on the same topic, also released by the State Department, Mr Huebner said his own experience of the Ambassador training was, "a bit like someone spending 30 minutes explaining ice dancing, as though that would be sufficient to equip me to strap up and pirouette on ice when I later arrived at the packed arena".
Clinton is seeking the Democratic nomination for the presidential election, and has been caught up in controversy over her use of a private computer server for work emails.
Her opponents have claimed that the use of a private server during her time as Secretary of State, from 2009 to 2013, put US security at risk.
The US state department has since released thousands of emails.
