Whelan is alarmed at the way Portsmouth and Hull have managed their businesses.
Portsmouth have debts totalling a staggering £119million while Hull, who visit the DW Stadium on Monday, have some major cash issues to address ahead of next season.
"When clubs get into financial difficulties, it is so sad and depressing," said Whelan.
"It is up to the directors like myself to keep the clubs afloat, keep them in reasonable order.
"Wigan are not going to slip down the path of Portsmouth or Hull, who seem to be in trouble. We have a debt, we will keep it and not increase it.
"The financial rules for Premier League clubs should be much stiffer. But they can be done quite simply, by limiting what each club can borrow to 25% of their turnover.
"You cannot borrow any more than it. If you do, you get a points deduction. It is easy to look at your turnover, it is easy to look at your borrowing.
"Twice a year the Premier League should look at each club's accounts. If your turnover is £45million, you can borrow £10million, no more."
Whelan is proud both of the way Wigan are run and of the fact they have secured their top-flight status for a sixth successive season.
He admits selling Antonio Valencia to Manchester United for £16million and Wilson Palacios to Tottenham for £11million in the space of six months last year were huge bonuses for the club.
Whelan said: "We have a good scouting system that works. We have brought some quality young players in and sold them. We are in business because of that.
"We have to look for youngsters, bring them on, play them in the Premier League and give them experience.
"If they have the ability, the bigger teams will bite and buy them. That has happened and saved us from all kinds of trouble.
"When you get £16million for one player and £11million for another in one season that is fantastic scouting and fantastic business on behalf of the club.
"We have to balance the books. We have to compete. Our most popular season ticket is £250, which is a third of the price of Manchester United and Chelsea.
"We have to manage things in a different way."
Meanwhile, manager Roberto Martinez is expecting a tough encounter against Hull on Monday.
He said: "From the outside you never really know what is going on at other football clubs and facing relegation is always a tough period.
"It is something you don't want to see anyone going through, but in football, and especially in the Premier League, you don't get any easy games.
"I think it will be a real focused performance from Hull and we will have to be ready."