James and Jennifer Crumbley are accused of ignoring warning signs before the rampage that left four students dead.
They have been charged with involuntary manslaughter, but failed to show for their arraignment on Friday.
Ethan Crumbley, 15, is accused of using his father's gun to shoot classmates in Michigan. He has pleaded not guilty.
Authorities have issued a fugitive warrant for the couple, and told US media they had launched a search after the Crumbleys' lawyers were unable to reach them by phone.
Oakland County Sheriff Michael Bouchard said the FBI and US Marshals Service joined the search for the couple.
But in a joint statement via text message to the BBC, lawyers Shannon Smith and Mariell Lehman said the Crumbleys were not fleeing law enforcement.
He said they had left town on the night of the shooting "for their own safety".
Their son is accused of opening fire on fellow students and teachers at his school in Oxford, about 35 miles (60 km) north of Detroit, on Tuesday.
The four killed were Tate Myre, 16, Madisyn Baldwin, 17, Hana St Juliana, 14, and Justin Shilling, 17. Seven others were injured.
Ethan Crumbley is being charged as an adult, and is facing one count of terrorism, four counts of first-degree murder, seven counts of assaults with intent to murder and 12 counts of possession of a firearm.
Why have the parents been charged?
On Friday, Oakland County lead prosecutor Karen McDonald acknowledged that charging parents in a child's alleged crime was highly unusual.
According to her office's investigation, the boy was with his father last Friday when Mr Crumbley bought the firearm believed to have been used in the shooting.
A post on the boy's social media later that day showed off his dad's new weapon as "my new beauty", adding a heart emoji.
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Just one day before the shooting, a teacher said she saw the boy searching online for ammunition, which prompted a meeting with school officials, Ms McDonald said. After being informed of the incident, Mrs Crumbley texted her son: "LOL I'm not mad at you. You have to learn not to get caught."
And on Tuesday morning - hours before the rampage - Mr and Mrs Crumbley were called into the school for an urgent meeting after teachers found a note by their son, including several drawings of guns and bloodied people alongside captions like "the thoughts won't stop. Help me", and "blood everywhere". The boy had also written "My life is useless" and "The world is dead", according to the prosecutor.
School officials told the pair they would have to seek counselling for their son.
But the boy's parents did not want him to be removed from school that day, Ms McDonald said, and did not ask him whether he had the gun with him, or search his backpack.
At 13:22 later that day, Mrs Crumbley texted her son to say: "Ethan, don't do it." Minutes later her husband called police to report his gun was missing, said the prosecutor.
But authorities say the boy had already emerged from the school bathroom and opened fire on fellow students.
Ms McDonald said the charges were meant to hold the Crumbleys accountable and to send a message about responsible gun ownership.
"The notion that a parent could read those words and also know that their son had access to a deadly weapon that they gave him is unconscionable, and it's criminal," she said.
The prosecutor had previously noted that, although the gun had been purchased legally, it "seems to have just been freely available" for the child's use. According to her, the suspect took the gun from an unlocked drawer in his parents' bedroom and brought it to school.
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