Face of Nation : PIP replaced the Disability Living Allowance (DLA) benefit in June 2016.
The ombudsman Marie Anderson can investigate suspected maladministration in public services.
The Department for Communities said only 12 out of 180,000 decisions have been referred to it by the ombudsman.
Ms Anderson’s decision follows a proposal sent to the department in January, in which she said she had received a “significant number of complaints about PIP” since June 2016.
She also pointed out that a “high number” of the department’s decisions on PIP applications had been subsequently overturned by an appeal tribunal.
The PIP investigation is the first time that the ombudsman will use her “own initiative” investigatory powers since they were granted under the Public Service Ombudsman Act (Northern Ireland) 2016.
Ms Anderson said her investigation would examine the “availability and application” of evidence such as GPs’ records and carers’ reports in the “decision-making and complaints processes”.
The department said it understood that the “introduction of a change on the scale of PIP can cause anxiety and stress for those affected”.
It added: “We are committed to ensuring we get decisions right first time and in the vast majority of cases that already happens.”
Improvements have or are about to be introduced after independent reviews of the PIP system, it said.
