The Whanganui District Health Board says the three people who have recovered from Covid-19 and since left the region were given authorisation to do so on compassionate grounds.
On Thursday it was announced all seven confirmed cases of Covid-19 in the region had recovered and were "now subject to Alert Level 4 restrictions".
Under level 4, movement between regions is restricted and authorities have put an emphasis on controlling the border with only essential workers moving between regions.
The WDHB said three cases who left the region were from the Ruapehu district, had fully recovered and were allowed to leave on compassionate grounds.
"They had a letter of authorisation to allow this," a statement said.
In response to questions from the Chronicle about criteria people need to meet to be able to move between regions on compassionate grounds the DHB said it "is a decision made locally by public health who have been monitoring them during their isolation. It is a decision made on the good judgment of those closest to the case".