In a special report released early on Wednesday, the comptroller, Micha Lindenstrauss, wrote that government officials were guilty of "serious failures ... that negatively affected the evacuees and caused unnecessary suffering".
The report said poor planning and handling of the evacuees led to a situation in which 40% were still in temporary quarters in hotels three months after the pullout, though the Prime Minister's Office, in charge of the operation, expected the settlers to stay in the hotels for only two weeks.
Also, the special administration set up to deal with the settlers "failed to achieve one of the main goals of the project, solving social problems", the comptroller wrote.
The report found that the government rented 840 apartments in Israel for the settlers at a cost of $1.1 million, but only 63 families moved into them.
Israel evacuated about 8500 settlers from 21 settlements in the Gaza Strip and four in the West Bank during a three-week period beginning in mid-August last year.
Many settlers rejected the government decision and refused to plan for or co-operate with their evacuation, offering mostly passive resistance to troops and police who came to haul them out.
The comptroller also leveled criticism at the leadership of the settlers for refusing to co-operate with the government office handing the evacuation, making it more difficult for the authorities to plan properly.