San Jose police believe the body of a girl found at a recycling facility on Charles Street on Saturday belongs to Ellie.
"We did locate a 3-year-old juvenile who was not conscious nor breathing and determined that female was deceased," said Sargent Jorge Garibay with San Jose police.
He added, "Officers on scene did believe that the three year old that we located was Ellie Lorenzo."
RELATED: Mother of Ellie Lorenzo confirms death of missing 3-year-old daughter
Mother of Ellie Lorenzo confirms death of 3-year-old daughter
On Friday, Ellie's mom requested a welfare check after the 3-year-old's dad did not show up for a custody swap.
The girl's father was later found dead in San Francisco.
"In speaking with the neighboring agencies, I was able to confirm that the father was found deceased of apparent suicide in San Francisco," said Sargent Garibay.
The father lived at an apartment complex in Fremont.
Over the weekend, Fremont police looked for Ellie at the complex.
On Monday, neighbors were shocked to learn of the homicide investigation and suicide of the father.
"How people can kill their own children," said Catherine Atrotter, Fremont resident.
RELATED: Fremont police looking for missing 3-year-old girl
Fremont police looking for missing 3-year-old girl
Some neighbors questioning why Fremont police did not deploy an Amber Alert for the missing 3 year old.
"As soon as I saw it my heart dropped. It's just awful," said Charles Green, Fremont Resident.
Multiple police agencies distributed the child's photo on social media as Fremont police searched for the father and the child.
"The Fremont Police Department has pursued several leads including contacting all friends and family members in the father's phone. We have done numerous welfares checks both in the Bay Area and in Southern California. We have reached out to numerous law enforcement partners through the Bay Area and the state," said Sargent Kim Macdonald with the Fremont police.
On the phone, Fremont police said this case did not qualify for an Amber Alert.
Marc Klaas, president of the Klaas Kids Foundation said more people should've been looking for Ellie.
"The way I understand it. She contacted the police for a welfare check because the child hadn't been returned. They found the father deceased without the baby and the baby is completely missing. I think that completely fits into the criteria right there," said Klaas.
Now three law enforcement agencies are collaborating to figure out what happened to Ellie while her family grieves her passing.
"We don't believe there is a public safety threat. We do believe that we have an idea of what occurred, and this is an isolated incident," said Sargent Garibay.
Ellie's family has set up a GoFundMe to help with her funeral expenses.