The Northern Ireland Police Ombudsman is to re-start investigations into 150 unsolved murders linked to the Troubles.
Dr Michael Maguire said new structures had been put in place to help deal with complaints about sensitive and complex cold cases.
Dr Maguire said: "Under the law, the PSNI's Historical Enquiries Team has had to refer certain incidents during the Troubles to my office for independent investigation. Members of the public across the community have also made complaints about serious matters, including deaths, during this period. It is important that these matters are dealt with."
Work on historical cases was suspended in September 2011 after the Criminal Justice Inspectorate (CJI) raised concerns about the handling of controversial high profile cases. The CJI found reports had been heavily influenced and buffeted by feedback from non-governmental organisations, families, their legal representatives and the Police Service of Northern Ireland (PSNI). There was also an inconsistent approach to how families were briefed.
Chief executive Sam Pollock also resigned, claiming the Ombudsman's office lacked independence. In its latest report, the CJI said public confidence in the Police Ombudsman's office had been restored. Inspectors found substantial progress had been made since Dr Michael Maguire was appointed last July. They also said there was a sea change within the organisation since the departure of Canadian Al Hutchinson and noted new quality assurance processes had been implemented.
CJI chief inspector Brendan McGuigan said: "This review found evidence that substantial progress had been made against our initial recommendations since September 2011. New structures and processes had been put in place within the OPONI (Office of Police Ombudsman Northern Ireland), which focused on providing comprehensive and robust quality assurance of investigations into historical cases and the subsequent production of public reports.
"Given the important role the OPONI has in terms of providing independent oversight of policing in Northern Ireland and the impact this has on public confidence, it is my intention to return to this issue again when a number of historic reports have progressed through the process and been published."
The Ombudsman's historic investigations unit, which has a staff of 40 and an annual budget of £2 million, will now look into allegations of police involvement in criminality between 1968 and 1998. It is expected to complete two complex investigations - some of which may be linked to 20 others - and six stand-alone cases each year.
According to the CJI, the history department's skills base had been enhanced by the recruitment of experienced senior investigating officers. This was the first time the CJI has published a report since Dr Maguire, a former CJI chief inspector, took up his post as Ombudsman.
Justice Minister David Ford welcomed the resumption of historic investigations by the Police Ombudsman. He said: "I am conscious of the distress the decision to suspend the investigations caused the families, police and the wider public. It is however vitally important that there is public confidence in the way in which investigations are carried out and reported."