Top flight English clubs last month approved the introduction of limits on losses and curbs on increases in player wages to try to ensure that the latest television cash windfall leads to greater financial stability.
"We believe very strongly that each club should continue to be permitted to run their business - including their pay rolls - as they see fit," Cortese said in a statement.
"This is fundamental to the future integrity of football," added Cortese, a Swiss-Italian former banker who has run Southampton for the past four years.
Cortese said Southampton, back in the top flight this season, were already operating "within the spirit" of the new rules, which are themselves inspired by UEFA's Financial Fair Play curbs for Europe's top clubs.
The club made a net profit of 900,000 pounds ($1.35 million) in the six months to the end of December. It was the first time since 2005 that they have had a surplus without the aid of additional income from selling players.
The value of a Premier League place was underlined by an almost trebling of revenues to 33.1 million pounds in the last six months of last year. Southampton are currently 16th in the 20-team league, just above the relegation zone.
Southampton have had a remarkable revival since German-born businessman Markus Liebherr bought the club out of administration four years ago, putting Cortese in charge of the day-to-day running of the club.
Liebherr died in 2010 but his family have continued to support the south coast club. Back-to-back promotions have been earned, helped by a total investment of 38 million pounds from the owners.
($1 = 0.6645 British pounds)