It comes after Labour's deputy leader Carmel Sepuloni made allegations in the House last week about Stephenson's interests in the pharmaceutical industry, and his role advising Seymour on Pharmac funding.
Speaking under Parliamentary privilege in the debating chamber, she described Stephenson as a "pharmaceutical industry plant".
His pecuniary interests declaration showed he had holdings in healthcare companies Chimeric Therapeutics, CSL Limited and Johnson & Johnson.
In a statement, Stephenson said the allegation was outrageous and completely baseless, and his role had no decision-making powers.
"There is no conflict between my declared shareholdings and the work I have been doing to support David Seymour as the Associate Health Minister," he said.
"That's because the role of Parliamentary Private Secretary is a non-executive role without decision-making powers - its purpose is to build relationships with relevant communities, represent the Minister at public events, and assist with administrative matters.
"The allegation made by Labour's Deputy Leader also shows she doesn't understand how Pharmac operates. Pharmac does not share information about specific drugs with Ministers, and Ministers have no ability to influence Pharmac's decision-making process."
He said he took his role as Private Secretary and MP "extremely seriously", and had been "consistently open and transparent about the meetings I have attended and have declared my shareholdings in the pecuniary interests register".
"I will not allow anything to distract from the Government's goal of delivering real change in the critical area of medicines access. I've decided to divest all my shareholdings as reported in the pecuniary interests register to ensure no distraction exists. I look forward to continuing my work with David Seymour as his Parliamentary Private Secretary."
Stephenson - a list MP - is the ACT Party whip, and its spokesperson for eight portfolios including health.
