Police hold serious concerns for the welfare of Jayden Brady, 14, and his brother Joseph, 11.
The pair were last seen at a home in Tweed Heads, in far northern NSW, about 3am (AEST) on Sunday.
Police allege the father had breached a court order preventing him from having access to his sons.
A man, 38, was arrested at Byron Bay on Monday but the children are yet to be found.
"The father is allegedly not assisting police with inquiries," NSW police said in a statement on Wednesday.
Acting Superintendent Shane Cribb from the Tweed Heads-Byron local area command says there are serious concerns their welfare.
"At this stage, we have got no idea where the boys are," he told Nine Network.
"The family is quite distraught."
Jayden is described as being of Caucasian appearance, between 120 and 140cm tall with a thin build, brown hair and eyes.
Joseph is also between 120 and 140cm tall with a thin build and brown hair.
Police confirmed a man was on bail after appearing in the Lismore Local Court on Tuesday for allegedly breaching a domestic violence order.
A spokeswoman said detectives had an address where the man was supposed to reside as part of his bail, and would make further inquiries with him later on Wednesday.
Police have appealed for public help to find the children ahead of a press conference at Tweed Heads police station at 9am (AEST).
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