A 40-year-old man who was known to both victims was charged with the murders and a 64-year man was charged with being an accessory after the fact to both murders.
Ms Faizal Pakeeza and Jojo were not reported missing to police until last January and an investigation revealed the pair had been subject to foul play.
Human remains were found under the Takapuna Landing Bridge on Saturday, police said.
Mr Lynch said today that Ms Faizal's mother alerted police to her daughter and granddaughter's disappearance in January, 2013.
"We believe they were killed at an address in Howick where Pakeeza and Jojo were living," Mr Lynch said.
Mr Lynch said there had been no earlier pleas to the public for information in the case.
Before police were alerted, Jojo's father had been desperately trying to find her and enlisted the help of a private investigator.
"Jojo's father did not have custody... He had make enquiries to find Jojo."
Mr Lynch would not reveal how police had come to locate the remains.
He said the two charged men were related to each other but would not reveal how the pair were connected to Ms Faizal and Jojo.
Charge sheets indicate the pair were killed some time between December 19, 2006 and February 9, 2007.
Mr Lynch said the discovery of the bodies had answered some questions the family had had for many years.
"For them it was around providing some answers."
He said a team of around dozen search specialists, ESR units and pathologists were at the site where the remains were discovered in Takapuna and it could be some time before they were recovered.
"I'd say they were one metre to one and half metres under ground."
The ground was full of mud and silt, he said.
Both men appeared in court separately, one after the other, and received interim name suppression.
One was remanded in custody until November 5. A decision on the other would be made this afternoon.
Jojo was believed to have been three years old when she was killed. Photo / Police
A lengthy investigation revealed the pair had been subject to "foul play", and human remains were found under the Takapuna Landing Bridge on Saturday, police said.
Police have cordoned off a section of the mangroves between the Akoranga Park & Ride station and Barrys Point Reserve.
About four police officers dressed in overalls are wading through the muddy creek.
A tent has been set up next to the station carpark.
The Golf Warehouse and Driving Range is located on the reserve and it also backs on to Rosmini College, the Lake House Arts Centre and The lake House Cafe.
A sifting tray, about a metre long, has been tied to the underside of a bridge, part of a track known as the Takapuna Landing, which connects the station and the reserve.
Mud was being loaded onto the tray by officers and then a hose was being sprayed onto the tray to sift through the mud.
David Feeney, assistant manager at Golf Warehouse driving range and shop, which borders the creek where police are working said police had not spoken to him about the case.
Mr Feeney said the area was quiet but there was a steady stream of university students around the reserve throughout the day and evening.
The driving range was also open until 8pm or 9pm. Police officers also often trained their dogs in the reserve.
Lisa Rogers, manager of The Lake House Art Centre, had also not been visited by police.
Miss Rogers said the reserve was usually quiet but there was a lot of foot traffic to the businesses.
She and other staff at the centre were shocked when told of the discovery.
Formal identification of the remains would be a "slow process" but police were confident they were connected to the investigation.
Detective Inspector Dave Lynch said the delay in the missing persons report was a significant challenge to the investigation.
"A number of avenues of investigation that would have been available to us at the time were unable to be followed due to the delay," he said.
"The result we have today was achieved due to the dedication and commitment of the Police team that worked for almost two years on providing answers for Jojo and Pakeeza's family."
- additional reporting Nicholas Jones, Sam Boyer
