"He shouldn't have left here in the first place, but he wanted to," said Allardyce, who reluctantly sold him to Middlesbrough in a 3.5m deal.
"He wanted to go chasing what he thought was a bigger club and bigger money."
Allardyce also told the Bolton Evening News: "The way we look after players here is unique.
"We put so much emphasis and so much money and research into it that we manage to keep players extremely fit.
"For Michael that was a loss. That loss has escalated in three or four years in him being cast aside by Southend and, for a lad of his talent and at his age, he's only got himself to blame."
Meanwhile, Sam Allardyce has challenged Greek midfielder Stelios Giannakopoulos to lift his game if he wants to break back into the first team.
Allardyce said: "He was our star man in many ways last season with his performances and goals.
"But Stelios has not lifted himself to that level again and he is finding that hard to deal with."