"All the nurses were quite on edge about it. Everyone was keeping their distance and being quite nervy."
He remained in isolation for the next three-and-a-half hours, he said.
His father-in-law was also placed in isolation while staff tested them for signs of the deadly disease.
"If I had a fever, they said I might have to spend 21 days in isolation and I don't know about 21 days with my father-in-law. He's a lovely guy, but 21 days is a long time," he said.
A Southern District Health Board spokeswoman said it disputed the version of events, but declined to comment on individuals due to patient privacy.
No one had been isolated or checked for Ebola in the Southern district, she said.
"SDHB had no cases of suspected Ebola and the local Ebola response had not been activated."
The disease has killed more than 4900 people in West Africa. No suspected cases have been reported in New Zealand.
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Mr Johnstone said "it was good to see Dunedin was well prepared".
He was clear of any symptoms and the situation was "all a bit of a laugh".
However, the infection which prompted Mr Johnstone's return from missionary work in West Africa was not so funny.
He broke a toe while working and an infection had spread to the bone.
"Burkina [Faso's] health services aren't the greatest, so we came back to get it fixed," he said.
"If we stayed in Burkina, it [the toe] would have been taken off - so it's always nice to keep it."
After being cleared of any serious illness, he was able to see a specialist and was prescribed antibiotics.
He would have surgery on his toe, which would take a month or two to heal, he said.
The family would head back to Burkina Faso to continue their missionary work in the north of the country once Mr Johnstone had a clean bill of health.
Despite some political upheaval in the country and the danger of Ebola in nearby Sierra Leone, Guinea and Liberia, the family was looking forward to returning.
"We feel fully safe up in the north of Burkina Faso," Mr Johnstone said.
"It's kind of like living in rural New Zealand. Everyone knows everyone."
SDHB medical officer of health Dr Keith Reid said the risk of infection in New Zealand was low.
"We continue to develop our plans for dealing with cases identified at the border or presenting to health facilities," he said.
"These are under regular review in light of evolving national guidance and the changing international situation.
"However, our current plans are up to the task of identifying a suspected case of Ebola within the Southern District and for providing any immediately required care while arranging for transfer to Christchurch Hospital, which is the designated treatment centre for Ebola on the South Island."
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