The names of the 431 prisoners were released by the IPS to allow civilians the opportunity to contest the release of individual prisoners in the courts. Additionally, the release of some of the prisoners requires the approval of the relevant army commanders or the president.
The release is expected to take place before next Tuesday, the date of a US-sponsored conference on Palestinian statehood set to take place in Annapolis, Maryland.
Eight of the nine prisoners whose release was rejected were found to have switched their allegiance from Abbas' Fatah faction to rival Islamist group Hamas which refuses to deal with Israel.
The release of a ninth inmate was rejected because he had previously escaped from jail before being recaptured.
On Wednesday, the IPS will hold a meeting to discuss the release process. It is likely that the prisoners will be transferred to the Ketziot prison in the south before their release, where they will undergo medical checkups, meet with Red Cross representatives and sign a document stating they pledge not to engage in terrorist activity in the future.