Macdonald, who was living in Mangere Bridge, South Auckland, disappeared some time before Christmas that year.
He had a history of disappearing after facing child abuse charges.
Macdonald was reportedly living in Portugal's Algarve region when 3-year-old Madeleine disappeared in 2007.
It was understood Macdonald was deported from Portugal to Australia in 2010 to face charges of raping an 8-year-old girl in 1989.
While on bail, he fled to New Zealand - and while on bail in New Zealand, he fled again.
He was arrested in the Algarve in 2010 on an international arrest warrant, English newspaper the Telegraph reported.
Macdonald served a six-month sentence in Australia for indecent assault.
He then moved to Brighton, where in June 2012 he was accused of abusing two sisters, aged 5 and 7. He was convicted, but fled yet again before sentencing.
He is now wanted in the UK for absconding, and for failing to notify authorities he had changed his name, his address and was going abroad.
New Zealand police last week confirmed the paedophile was the subject of active arrest warrants here.
Macdonald is also wanted for failing to appear in court, and a charge under the Passport
Act.
Warrants for his arrest were issued at Auckland, Hamilton, and Waitakere district courts.
He was known in New Zealand as Roderick Robinson, police said last week.
He changed his name to Macdonald after being convicted of child sex offences in the UK, British newspaper the Telegraph reported.
Macdonald was caught in Malta this month after four years on the run following a conviction for abusing two girls in Brighton, England.
New Zealand police said they'd been in contact with British law enforcement agencies in recent weeks.
