The search operation was launched involving police from Deniliquin Local Area Command, SES, and Maritime Rescue, and the Victorian police airwing.
Victoria Police divers are due at the Murray River by 9am to continue searching for the boy after initial attempts to find him last night failed.
"Following an ongoing search effort, the body of a child was located in the water about 11.35am today", a statement from NSW Police said.
The 27-year-old woman didn't appear before Deniliquin local court as expected on Saturday morning after requesting to stay in the custody cells.
She has been charged with attempted murder after allegedly taking the two boys to the river in Moama, on the NSW-Victoria border.
Police alleged the woman took her children to the Murray River and told her eldest son (9) to get into water before she tried to drown him.
Detective Sergeant Swinton told the court the younger son was screaming during the incident. The older boy managed to struggle free when the woman turned to the younger boy.
She then allegedly attempted to drown the younger son, who was last seen drifting face-down in the water.
A dog that belonged to a nearby property owner then bit the boy as he fled up the riverbank. Screams were heard by people on the riverbank who did not witness the incident.
It is understood the nine-year-old boy sustained several dog bites and is in a serious condition in the Royal Children's Hospital in Melbourne.
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The woman, from Deniliquin, is expected to be extradited from Victoria to NSW to face charges after handing herself in to police at Echuca on Thursday night.
"She's pretty upset", the Legal Aid duty solicitor said outside the court. Mr Hebbard said it was too early to say if his client plans to fight the charge against her.
Lawyers for the boys' grandmother said their client blames the Department of Community Corrections and the police for the tragedy, after their "lack of communication and support in essentially off-loading the housing of her daughter to our client".
A Saturday morning court hearing heard the mother is likely to be charged with more offences. The court heard how she allegedly told witnesses the night before the incident that she "had to drown my babies".
A neighbour outside the court on Saturday, said it was impossible to imagine what the grandmother of the children was going through.
Lawyer Dale Brooks, who is representing the grandmother of the boys, told news.com.au the 27-year-old was a long-time ice addict and well-known to local authorities.
He described the response as "absolutely nil".
Shortly after, Brooks said the woman took the grandmother's vehicle, snatched the two young boys and left with a couple of her buddies.
The accused is said to have been living in a caravan at the back of the grandmother's property after her prison release, despite a 12-month Apprehended Violence Order (AVO) taken out against her by the grandmother in May 2016.
"It's a bad story, it's a sad story".