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A man shot dead in South Australia, a woman drowned near Perth, a car park brawl death in the West Australian town of Shark Bay and an alleged rape in Hobart have marred New Year celebrations across the nation.
Despite the violent incidents, police were happy with the behaviour of revellers, saying the majority of people were well behaved.
An estimated 1.6 million people flocked to Sydney's harbour foreshore and 550,000 people packed into Melbourne's CBD to watch the fireworks.
In Sydney, 97 people will face a range of charges including drug supply and possession, assault, affray, assaulting police and malicious damage.
That was almost double the number arrested in Sydney last year but police said they were happy with the outcome.
At the major public celebrations in Adelaide and South Australian regional centres, police made 121 arrests for offensive behaviour.
The number includes the arrest of a 17-year-old who is expected to be charged with murder, following the shooting death of an 18-year-old at about 7.40pm (local time).
South Australian police said most revellers partied "safely and lawfully".
In WA, a 31-year-old man in Shark Bay has been charged with grievous bodily harm after a 28-year-old man died after allegedly being punched in a car park brawl.
In the state's south, the body of a woman was found floating in a weir east of Perth.
There were seven stabbings in Brisbane and more than 30 drug overdoses across Victoria, including a 15-year-old boy.
Police arrested 62 people on 89 charges in Brisbane and 184 people on 218 charges on the Gold Coast.
Victorian police arrested 356 people across the state, but Deputy Commissioner Tim Cartwright said it was an improvement on the 400 arrests of drunk people in 2010.
In Tasmania, a man has been charged in connection with an alleged rape close to the centre of Hobart's New Year's Eve celebrations.
Police have interviewed and charged a 35-year-old man following a complaint from a 26-year-old woman about the alleged incident near Tasmania's Parliament House.
Sydney Lord Mayor Clover Moore praised organisers, clean-up crews and the city's residents for a "magic" New Year's Eve celebration on the harbour.
"Sydney is really special and it is the New Year's Eve capital of the world, we just all know that," Ms Moore said on Tuesday morning, adding that given the numbers of people out to celebrate it was amazing that police had charged only 97 people across Sydney.
Pop superstar Kylie Minogue said Sydney's celebration to welcome in 2013 was a highlight of her life.
The Sydney fireworks show paid homage to the diminutive singer, whose hit tunes from her 25 years in show business featured in the soundtrack.
Her red lips in lights on the Sydney Harbour Bridge puckered up at midnight to deliver a kiss to welcome in the new year.
"The atmosphere was electric and it was a night I will never forget," Minogue said in a statement on Tuesday.
"Sydney has the reputation as the New Year's Eve capital of the world and it certainly lived up to that promise last night."