"There have been reports of probation staff being verbally abused and assaulted as a result of applying the sanction, " she added.
If an offender fails to comply with a court order, probation staff will have no hesitation in returning them to court to be resentenced or given additional punishment.
The revised project still aimed to provide prison and probation staff with improved access to the information they needed "to effectively manage offenders in custody and in the community", he said.
But Justice Secretary Ken Clarke blamed Labour for the "historic" problem with probation staff spending too much time on paperwork and suggested Mr Khan was "in denial" about the UK's "deficit problem".
BBC: Probation staff 'spend just 24% of time with offenders'
"I am issuing guidance to both prisons and probation staff to highlight the need to avoid over-emphasis on good behaviour in prison and the progress in addressing what are called dynamic risk factors when assessing risk prior to release, " he said.
He said the last 10 years had seen a "massive rise in the constant government monitoring of probation staff, to the detriment of face-to-face contact with offenders" which, he said, "does not enhance public protection but undermines it" and should be reversed.
BBC: Probation staff 'spend just 24% of time with offenders'
It included plans for putting the bottom 10% of staff on probation and fired after a year if they fail to improve and ministers being given the power to choose who runs departments.
In June, Cabinet Office minister Francis Maude published a package of reforms to the civil service, including plans for putting the bottom 10% of staff on probation and fired after a year if they fail to improve and ministers being given the power to choose who runs departments.
Government plans to reform the civil service, including putting 10% of staff on annual probation, have caused controversy.
Mr Clarke said he was about to pilot some "payment by results" contracts in the probation service - already in place in two prisons - and give staff the discretion to work in ways to best reduce the number of crimes committed by people released from prison.
BBC: Probation staff 'spend just 24% of time with offenders'
He said his staff is in regular contact with the state Parole and county Probation departments.
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