A man has been charged with sexual assault after an alleged domestic dispute in Grafton in northern NSW.

A 29-year-old man is facing a range of assault charges after a domestic dispute in northern NSW.

Police began searching for the man after he picked his four-year-old son up from a local childcare centre in Grafton on Monday afternoon and did not return him to his mother.

The pair were found in South Grafton just before 7.30am on Tuesday when police stopped the man’s Toyota Hilux four-wheel-drive.

The boy was found in the back seat of the car and was reunited, unharmed, with his mother.

His father has been charged with two counts of sexual assault, one count of indecent assault and with breaching an apprehended violence order.

Police will allege the sexual assault occurred after a domestic argument.

The man was refused bail and was due to appear in Grafton Local Court on Tuesday afternoon.