Missing William Tyrrell's biological father has faced court over an intimidation charge and an apprehended violence order (AVO) taken out by his own family.

Brendan Collins, 36, who has been back behind bars since September faced a charge of stalk and intimidate with intent to cause fear of physical or mental harm against his mother.

Collins, who is estranged from William Tyrrell's birth mother Karlie Tyrrell, has an interim AVO taken out by police on behalf of his mother Natalie Collins.

In Burwood Local Court on Monday, prosecutors agreed to drop the intimidation charge with the establishment of a permanent AVO against Collins by his mother.

Brendan Collins appeared in court on an AVO order taken out by his own mother. Photo / News Corp
Brendan Collins appeared in court on an AVO order taken out by his own mother. Photo / News Corp

Magistrate Leanne Robinson granted a two-year AVO by Natalie Collins against her son.

Wearing a tracksuit and white sandshoes, Collins thanked the magistrate who granted his lawyer's request he be released from custody.

Collins had previously been refused bail after serving seven months in prison for drug and theft offences.

In February, Bankstown Magistrate Kathy Crittenden acknowledged that Collins had suffered under the weight of his son's 2014 abduction.

Collins was then convicted of eight charges of having stolen items in his possession including bank cards, toys, novelty items and clothing.

He was also convicted of minor drug possession after police found him with a "minuscule" amount of methamphetamine, or ice and a glass pipe.

Crittenden heard Collins had suffered from "flashbacks and psychological and emotional problems" since his then three-year-old son William vanished on September 12, 2014.

News.com.au revealed exclusively how Collins' life has unravelled since that day, with his descent into drugs, crime and mental health problems.

Brendan Collins laid bare harrowing details of his life since his missing son became the subject of Australia's biggest manhunt.

In Burwood Court on Monday, Magistrate Robinson warned Collins he must not assault, stalk or intimidate his mother or recklessly destroy her property.