The decision to shut out the public has also been sharply criticised by the federal government.
A Senate committee probing the growth of Australia's illicit tobacco trade on Monday stopped mid-hearing and asked health advocates to leave.
"We were giving evidence and the chairperson suspended the session and said 'please wait in the halls and we'll bring you back in'," Australian Council on Smoking and Health chief executive Laura Hunter told AAP.
"Well we came back a little bit earlier and we could hear that there was testimony given in the room.
"It was locked and the broadcast had been suspended, but we knew there was someone in there giving evidence, and we had significant concerns that it was Phillip Morris International."
Philip Morris is one of the three biggest tobacco companies operating legally in Australia, along with British American Tobacco and Imperial Brands.
It had made submissions to the committee, like many other interested parties.
However, the company's appearance before a Senate committee runs counter to an international agreement signed by Australia during John Howard's government.
The World Health Organisation convention requires signatory governments to limit interactions with tobacco companies to only when "strictly necessary" and to do so "transparently".
A health department guidance document - signed off during Scott Morrison's government - makes clear this applies to all public officials, including members of parliament.
Both Health Minister Mark Butler and public health advocates, including Ms Hunter, have stressed this point to the committee.
Mr Butler wrote to president of the Senate, Labor's Sue Lines, and committee chair, Liberal Senator Leah Blyth, to remind them of their obligations on May 1.
However, the Senate committee voted in private to allow the testimony, with Greens Senator Jordon Steele-John revealing it had taken place when the public hearing recommenced.
"We have just taken evidence in camera from Philip Morris. I shared with them during our exchanges my opposition to their presence at this inquiry," the West Australian Senator said.
The committee has six members: three Liberal, two Labor and one Green, with Senator Blyth as chair exercising a tie-breaking vote.
"The illicit tobacco crisis in Australia is multi-faceted and there is no one single solution," Senator Blyth said in a statement.
"We must be mindful not to silence those with whom we do not agree, especially in the case of businesses who are directly involved ... it doesn't make sense to have an inquiry into illicit tobacco and not hear from all entities impacted."
Assistant Health Minister Julian Hill questioned why the evidence needed to take place in private, linking the decision to campaign funding.
"What are the coalition trying to hide in their dealings with big tobacco?" he said.
"It's not the Labor party that take donations from big tobacco but the same can't be said of the coalition."
