He said the amount of money being spent by English and French teams represented a significant threat to the game in the southern hemisphere.
"We've already seen a mass exodus of players out of Africa and Australia and if it continues at the rate it is, I think it could impact all the other markets in SANZAAR." Marinos said.
The first year of the conference format drew plenty of criticism, especially around the draw with some sides not playing New Zealand teams and some teams hosting finals against sides which accumulated more points.
"The format is going to stay in conferences for the foreseeable future given our geographical challenges we've got," Marinos said in Sydney on Monday.
'It's more 'how do we get the competitiveness in the teams and understanding that it's not easy'. This is a blooming tough competition."
The draw for 2017 will be released today.
Australian representatives had the chance to air any grievances at this week's two-day meeting of coaches, CEOs and other stakeholders at the 2016 Super Rugby review in Sydney, but were apparently diplomatic.
"They were quite quiet to be honest but they understand where we are in the strategy," Marinos said.
Several Australian and South African sides struggled in the 2016 Super tournament, which was dominated by New Zealand teams, who took three of the four semi-final placings.
"It is a concern. It's been a concern for a while, but that's a national union objective around high performance plans and how they are getting their squads together," Marinos said.
Despite some of the negativity surrounding Super Rugby, Marinos was adamant there wasn't much wrong with the product, pointing to viewing figures and game statistics.
"I do tend to get the feeling especially in this market [Australia] and New Zealand and probably even in South Africa to a degree, people think the whole thing is broken, but it's not," Marinos said.
"It's a damn good competition."