"We knew there was a problem, but we never imagined it was this grave," one senior military officer was quoted as saying by the Yediot Aharonot daily.
The survey - which questioned 1,000 soldiers - was commissioned several months ago by the commander of Israel's central command, an army spokesman said.
As a result of the findings, all soldiers serving in the territories are to attend a two-day workshop. "We are making an effort so that the soldiers behave themselves better," a military source said.
Israeli checkpoints in the West Bank have mushroomed in the aftermath of the Palestinian uprising in September 2000 as the military intensified a crackdown on armed Palestinian fighters.
"Sometimes he tries to bypass you because that's what saves him his day of work - and then you catch him. What are you going to do to him? You're going to punish him"
The roadblocks, often manned by 18- to 21-year-old conscripts, dot the territory, severely hampering Palestinian freedom of movement, feeding local resentment and stirring widespread international criticism.
"When you prevent thousands of people from moving freely, that's something that can't be done nicely," Yediot Aharonot quoted one soldier as saying.
"What can you do, you can't expect the Palestinian citizen to say thank you for what you're doing to him," he said.
"Sometimes he tries to bypass you because that's what saves him his day of work - and then you catch him. What are you going to do to him? You're going to punish him," said the soldier.
"You can keep him there for eight hours to roast in the sun ... Things like that happen all the time. One time a truck driver lied to me that he had a permit, so I kept him on his knees for four hours."