Police have been searching for Ember, eight, Maverick, nine, and Jayda, 10, since December 2021, when they were taken by Phillips to an unknown location - though police believe it was in Western Waikato within Marokopa or the surrounding areas.
Tom Phillips does not have legal custody of the children and there is a warrant out for his arrest.
Posting on Facebook, their mother, known as Cat, said she was "well aware of the hateful rumours being spread around" and asked that people knew her before judging her.
She said she was sharing the letter to show that all was not as it seemed and to assure people that the children would be coming home to a loving and stable family.
Cat said she along with their two sisters, grandparents, aunties and cousins would be waiting for them.
The handwritten letter - which is not dated or signed and which RNZ has not been able to verify - describes the writer's love for Cat, apologises to her and says he has a good heart and means well.
"I know if I ever give up trying to make things right I will regret it forever," the letter says.
"Im sorry for everything I have ever said or done to hurt you," it says.
The letter goes on to say that "although I make multiple f*** ups I have a good heart and I mean well".
"We have an awesome family and thats [sic] worth fighting for," is the last line of the letter.
Cat said she had not spoken out earlier because she did not believe it would bring her children home, but the fact that police were now offering a substantial reward had given her the courage to break her silence.
On Tuesday Cat broke her silence to make a video appeal provided by police for people's help in returning the children to her.
Police have offered an $80,000 reward for information that would help discover the whereabouts of three children and lead to their safe return.
RNZ has contacted the police to verify whether they knew about the letter and whether they can confirm it is from Tom Phillips.
