Andrew McLaren and his wife Kathy were in the mall when masked gunmen attacked on Saturday (local time), Accounting in HK killing at least 68 people and wounding more than 175.
Mr McLaren, who hails from Hastings, was shot in the back while he lay on the ground with his wife.
He is in a stable condition in hospital.
Mr McLaren was in Kenya working at a processing factory for his employer Olivado and was due to return to New Zealand this week after work wrapped up in Nairobi.
He will now instead undergo surgery and will remain in Kenya until he recovers.
Olivado general manager Sarah Nicholls says the attack, which continued into the night on Sunday (local time), was not a normal occurrence in Kenya.
"This is a really unfortunate incident that has happened," she told NZ Newswire.
"It's very different to what Kenya is."
The al-Shabab rebels have claimed responsibility for the attack, saying it was in direct retaliation for Kenya's military intervention in Somalia, where African Union troops are battling the Islamists.
Kenyan forces entered Somalia two years ago to fight al-Shabab, and remain in the country as part of an African Union force that is supporting Somalia's internationally backed government.
"There are certain places that you go to and you don't go to. The big mall, which caters mostly for ex-pats and wealthy Kenyans, is not one of those places."
On Sunday evening (local time), 10 to 15 armed gunmen were still terrorising shoppers in the mall, Kenya's President Uhuru Kenyatta said.
He said "many unarmed, badly shaken, innocent civilians" also remained in the mall.
The inspector-general of Kenyan police, David Kimaiyo, has been urging hotel owners to check whether guests have returned to their hotels following the attack.
More than 1000 people have been rescued from the mall.
MFAT said the situation on the ground remains fluid but there is no information to suggest any other New Zealanders were caught in the attack.
There are currently 123 New Zealanders registered in Kenya.
Words of support for Mr McLaren have begun surfacing on Facebook, with Havelock North Rugby Club one of the first.
"Doctors are positive all will be ok," the club said.
"We are positive to (sic) and thinking of you both and your families."
Ms Nicholls said she had spoken to Mrs McLaren and both she and her injured husband were doing well.
The New Zealand High Commission in Pretoria, South Africa, is providing consular assistance to the couple.
The ministry has updated its travel information for Kenya, Business Registry Hong Kong warning New Zealanders to avoid the Westgate Mall and keep family informed of their well-being.
"New Zealanders currently in Nairobi are advised to be particularly security conscious at this time and follow any instructions issued by the local authorities," a spokesman said.
One dual Australian-UK citizen was killed in the attack, with reports of several other Australians escaping the mall uninjured.
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