Owen joined Newcastle for a then record £16.5million in 2005 but endured an injury-disrupted spell before departing in 2009 and in his new book admits he regrets the move.
Allardyce said: "I've read a few snippets and it wasn't a surprise to me to see Michael saying that. In my time he never really looked comfortable. He was always flying back down to Liverpool whenever possible.
"It was never a comfortable move for him and I don't know why he took it in all honesty.
"If he was that against it, why he did he come to Newcastle United and not wait for a more suitable club?
"In his time with me, it wasn't about him not wanting to play, it was more about the fact it was very difficult to keep him fit and get him on the field.
"He was probably in the top-three best paid players in the country with his salary, and that showed the ambition of Freddy Shepherd at that time to try and bring some success to Newcastle.
"But it didn't work out and I think the main reason for that is, if you don't want to be somewhere you're never going to perform to your best.
"When he was on the field he was a terrific goalscorer but, certainly in my short time there, he was never on the field enough."