Charges of willful harm to a child were filed against Bryce McIntosh and Jillian Godfrey for something that they did to their missing son, Noah McIntosh, on Feb. 24.
Bryce McIntosh is being held on $1 million bail while Godfrey's bail is $500,000.
An arraignment, where the couple is expected to be formally charged, was postponed to April 8.
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While Sgt. Chad Fountain says part of the case now centers on the criminal aspect of what happened to Noah, they're still trying to find him. More than 10 detectives are assigned to the case.
"I know they're working tirelessly. They've been here around the clock almost since Tuesday evening, after we were unable to make contact with Noah," Fountain said.
Corona police say their investigation began Tuesday when officers spoke with Godfrey and unsuccessfully tried to contact Bryce McIntosh at an apartment.
Officers serving a search warrant at the apartment Wednesday found McIntosh inside with his 11-year-old daughter, but Noah wasn't there.
Detectives then arrested McIntosh and Godfrey. It's unclear if they have attorneys.
If you have any information about Noah's whereabouts, you're urged to contact Senior Detective Mario Hernandez at (951) 279-3659 or email him at Mario.Hernandez@CoronaCA.gov.
The Associated Press contributed to this report.