An American father has been accused of murdering his three-year-old son because his teenage girlfriend disliked children and had threatened to leave him.

David Creato, 22, was charged with murder and endangering the welfare of a child on Tuesday following the discovery of his son Brendan’s body in Cooper River Park, New Jersey on October 13.

Creato had reported Brendan missing three hours earlier, claiming he’d woken up to find the boy missing from his home in Haddon Township.

“I just woke up and he wasn't in my apartment,” the dad told the police operator on a call obtained by 6ABC. “I don't know if he wandered out or what happened. I don't know where he is.

“The door was locked. I guess he unlocked it and left,” he added, telling officers that the boy was wearing only his pyjamas, neon socks and Mickey Mouse slippers when he vanished.

Three hours later, following a frantic search, officers found Brendan in Cooper River Park.

Brendan Creato’s body was found partially submerged in Cooper River Park, New Jersey (pictured) on October 13 (Google Images)

Prosecutors say he was a victim of 'homicidal violence' and appeared to have been smothered, strangled or drowned, thanks to bruising near his collarbone and his brain showed signs of oxygen deprivation before his death, according to NJ.com.

Creato was arrested on Monday with bail set at $750,000 as he is considered a potential flight risk.

Prosecutor Christine Shah conceded that the case against Creato was largely circumstantial and based on there being no signs of forced entry at the property and on the “intense” relationship Creato had with his 17-year-old girlfriend Julia Spensk.

Miss Spensk, prosecutors claim, had a serious dislike of children and resented Brendan getting in between her and Creato, who had custody of the boy every other weekend.

She is said to have told Creato that the visits got in the way of their love affair and told him she would break up with him unless he severed contact with both Brendan and the boy’s mother.

A GoFundMe account which set up after Brendan's death raised $19,407 towards his funeral costs.