Justice Tracey Walker told the jury panel this morning they were no longer required.
She advised the court Thompson had cut off her electronic monitoring and was now being sought by police.
She said while some jury trials could proceed without defendants, this was not one of them and she vacated the trial. She said a new trial date would be set once Thompson was found.
"And she will be located," Justice Walker told the jury panel.
Crown Solicitor Amanda Gordon said after the court hearing Thompson's bracelet had been removed on Thursday night last week.
She said it was frustrating when trials were put off as it cost a lot. She said in this case there were several expert medical witnesses who had "put their lives on hold" by cancelling clinics to be in court this week.
Thompson was charged with the toddler's murder in November 2019.
A Department of Corrections spokesperson said they were helping police to find Thompson who was on court-ordered bail.
"Corrections was aware of this immediately when a strap tamper alert was triggered. A field officer attended the sentence address and confirmed that the person had removed their tracker and absconded. Police were notified immediately."
A police spokesperson said they were actively looking for Thompson and a warrant to arrest was issued by the court.
Anyone with information about her whereabouts is asked to contact police via 111 and quote file number 210209/7336.
Alternatively, information can be provided anonymously via Crimestoppers on 0800 555 111.
