Ben Haim was expelled from coach Dror Kashtan's training camp in Slovenia last week after allegedly insisting he would not take part in training.
However Allardyce has now explained the circumstances behind Ben Haim's decision. "The name of one of our players has been blackened and because he has been so hurt in such an unfair way and has not spoken or reacted publicly I decided to support him openly," said Allardyce.
"On August 5 Bolton flew to Spain for a training camp and Ben Haim played for 90 minutes on the Tuesday and Thursday against both Huelva and Seville.
"But, when Ben Haim joined up with Israel on the following Friday, the conflict began.
"The Israel fitness coach asked Ben Haim what he had been doing over the previous few days and he explained about the two matches he had played and the fact that he had travelled for 13 hours the previous day.
"Ben Haim told him he needed time to recover and that he did not feel he should train that day, knowing that the team were not due to play until three days later.
"Ben Haim assured him he would be ready for a full training session the following day.
"Apparently, when Ben Haim turned up for training on the Sunday, fully fit and rested, they refused to allow him to join the other players so he trained by himself on another pitch.
"He was told he was suspended and that a flight had been arranged for him back to the UK that evening."
Meanwhile, Bolton have reportedly expressed an interest in Rangers defender Jose-Karl Pierre-Fanfan.