Prof Hoek said any comments in the debate should be scrutinised closely.
"We know the tobacco industry has funded ... groups in New Zealand [in the past]. That became very apparent during the whole debate over the removal of tobacco retail displays a couple of years ago," Prof Hoek said.
"So we know that they have their tentacles reaching out and that they are trying to create groups to give them a veneer of public respectability.
"I think we've got to scrutinise those sorts of claims very carefully."
IPI, which is funded by donations from businesses and individuals, released a paper voicing opposition to the Government's proposed plain packaging legislation, including what it says are implications on trademarks and overseas trade.
The IPI would not disclose the individuals and organisations that contribute to its $1.5 million per year funding, but BAT said it did not donate money to the organisation.
The US Chamber of Commerce, which says it represents "the interests of more than 3 million businesses of all sizes, sectors, and regions", also stated its opposition to the legislation and said there were alternatives to deal with the public health problems of smoking.
Prof Hoek said the university's research had revealed "pretty strong evidence that plain packaging is going to be good for health and that it will protect future generations of children from taking up smoking, which is, let's face it, a deadly addiction".
"I think what these organisations are trying to do is to muddy the waters because I think the waters are actually very clear and the research base is very strong," she said.
"I think we can rely heavily on people's common sense [to judge criticism of plain packaging]. I think they are trying to muddy the waters but I think they are being spectacularly unsuccessful in their attempts."