Mr Whelan, who is chairman of Wigan, said he had sold the shares ahead of tomorrow's Budget to take advantage of legislation on capital gains tax.
He said he feared that Gordon Brown, the Chancellor of the Exchequer, would end capital gains roll-over relief which limits or defers the tax payable provided the proceeds are invested in another business.
"I think the Chancellor will end that, so by selling now I will not have to pay the 40 per cent tax," Mr Whelan said.
"If there wasn't a Budget on Wednesday I wouldn't be selling."
Mr Whelan sold 3.5 million shares at 481p each. However, he and his family still control 55 per cent of the fast-growing company and Mr Whelan has undertaken to sell no more shares for 12 months.
He said his family remained as committed as ever to the company: "We still live and breathe it. We love it."
Mr Whelan will use the share proceeds to help fund a new pounds 20m stadium for Wigan which it will share with Orrell, the rugby union club.
Construction of the 25,000 all-seater stadium is expected to start in September and is scheduled to take 12 to 15 months.
Wigan were promoted to the second division of the football league last season and Mr Whelan said he was hoping for more success in the coming campaign.
"We are going to fight like hell for it," he said.
The share sale comes just two weeks after Mr Whelan gave his grandchildren pounds 28m of shares for inheritance tax reasons. The gift made two-week-old Paul Sharpe one of the youngest millionaires in Britain.
Separately JJB Sports issued an upbeat trading statement showing that in the 22 weeks to 29 June like-for-like sales were 18 per cent ahead of the same period last year.
Total sales, including new openings and additional floorspace, were 60 per cent higher. Though this is lower than the 71 per cent increase announced in April, the company said this was due to a relatively poor start to 1996 because of adverse weather conditions.
JJB shares were unchanged at 492.5p.