Callaghan was arrested in September last year after a three-month investigation into the disappearance of the 32-year-old.
Police found her remains in plastic containers buried in a shallow grave in bush off a walking track.
Callaghan made the plea at the High Court in Auckland today. Ms Thomas' family, some of who are in South Africa and the United Kingdom, have been told of the development.
A post-mortem examination showed Ms Thomas died from multiple blows to the head on the morning of June 29, 2010.
The fatal strike fractured her skull behind the right ear and the shock caused such severe damage to her brain stem it killed her.
Callaghan earlier pleaded not guilty to the murder of Thomas, and was due to stand trial next February.
He has been remanded in custody until next March for a disputed facts hearing.
Outside court, Detective Inspector Mark Benefield, the public face of the murder inquiry, said investigators worked hard to solve the case.
"It was difficult. We had some real issues, especially around the media, that caused us hard work but it's a pleasing day for the family and members of the team who have got to this result.''
Police had empathy for the victims, he said.
"We have a 5-year-old boy who has lost his father and mother, we have a mother who has lost her son, a mother who has lost her daughter.''
Crown Solicitor Simon Moore SC, who led the prosecution case, told media the guilty plea was very important for Ms Thomas family.
He said the guilty plea was helpful because it saved the community time and money of a trial but could not comment further because there was a sentencing process to go through.
"I think it is important that we don't say anything ... until the sentence is passed.''
Callaghan's barrister Stuart Grieve QC said: "Mr Callaghan is an intelligent young man who has taken responsibility for his actions in this tragic saga and has pleaded guilty to the two charges today which includes murder.''
He said it was a significant step for him to take but he had done so "responsibly''.
Callaghan and Ms Thomas had a young son together that they shared custody of. He is now being cared for by relatives.
- Andrew Koubaridis, New Zealand Herald
