|PNG Prime minister: Peter O'neill|
Mr O'Neill said there had been problems with every election in PNG since independence from Australia in 1975.
"The geography of PNG makes service delivery and communications an enormous challenge day in day out. Staging national elections across the country is no different," he said in a statement.
"I thought overall the conduct of the last election was significantly better than then 2007 election, and the 2002 one before that."
The 2002 election - in which 100 people were killed in election-related violence - is considered by some PNG observers as the benchmark for how bad elections can get.
The 2007 election introduced limited preferential voting, a move seen as limiting the violence surrounding the election period.
Mr O'Neill said an important check and balance to the electoral system was the court of disputed returns, where more than 100 petitions had been filed against winners in 89 electorates.
In its report on the 2012 election, TIPNG said 21 per cent of polling place observers rated the process unfair or very unfair, while 45 per cent said it was mostly fair.
Just 37 per cent of TIPNG's 282 election observers said the process was very fair.
The report also found a large number of people appeared to be disenfranchised as a result of roll inaccuracy and possibly wrongful removal from the roll.
"This brings into question if the will of the people was truly expressed," TIPNG said.
The report said Australia's support of on-time elections in the form of logistical aid was a sign the system had failed.
But Mr O'Neill said it was another sign of the democratic process at work in PNG.
"I believe that with Australian support, and the presence of international observers, as well as a free press, and a robust political party process, the election produced a fair and democratic result."
The 2012 poll returned Mr O'Neill to the prime ministership at the head of a 94 MP-strong coalition in PNG's 111-member parliament.
During the elections AAP witnessed children voting in the Highlands town of Tari, while in another incident a police officer told of how a mother and breastfeeding baby were given two ballots so both could vote.