"Everything is virtually agreed and the only reason it's not been signed up is because I'm in Majorca," Whelan told Sky Sports News.
"I'm due back on Wednesday and the deal will be completed on Wednesday afternoon, and we'll have a press conference on Thursday.
"It's 99 per cent certain that Roberto Martinez will be our new manager. Everything is in place and the contract will be a three-year deal."
Wigan were looking for a new head coach, following the departure of Steve Bruce who took charge of Sunderland days ago.
Martinez, who had a six-year spell at the JJB Stadium as a player, is regarded as one of the best young coaches, and was also approached by Scottish giants Celtic of late.
Excited
Whelan believes that Martinez could carve out a brilliant career in the Premiership, saying the club's fans have high expectations for him.
"I'm hoping that Roberto stays with us for quite a long time," the Wigan president stated.
"I was really sad to lose Steve Bruce, who was a great manager for Wigan Athletic, but Roberto was one of my 'three amigos' and he is a wonderful man and knows football inside out.
"He has done remarkably well at Swansea. We at Wigan, and all the supporters, are very, very excited at getting Roberto Martinez.
"The Premier League is the best league in the world and the most difficult league in the world to survive in.
"Roberto first came to us when Wigan were in the fourth division and he stayed with us for four or five years and he has gone and done wondrous things in management.
"There is no reason why he cannot come into Wigan and be a top quality manager in the Premier League. If I'm being very honest, I predict Roberto will go on to be one of the top four or six managers within four or five years."