According to Dr Michael Maguire, the PSNI has refused to provide information to the Police Ombudsman's Office, or requested explanations and justifications as to why the material is required.
It is claimed that such refusals have occurred more than 100 times, "despite repeated requests over past months", and that investigations into more than 60 deaths have been stalled as a result.
Dr Maguire has described the action as unusual and unfortunate, but necessary.
"The many thousands of people who make complaints to us every year do so on the basis that we have access to all the police information we need to independently investigate their complaint," he said.
"That principle is enshrined in law and accepted across the community. Investigation by negotiation is not acceptable."
We will continue to fulfil our legal obligations with the primary consideration being that of protecting life in accordance with Article 2 of the European Convention on Human Rights.
Section 66 of The Police (Northern Ireland) Act 2000 says that the Chief Constable "shall supply the Ombudsman with such information and documents as the Ombudsman may require for the purposes of, or in connection with, the exercise of any of his functions".
The Police Ombudsman intends to take legal action in the form of a judicial review.
In a statement, a PSNI spokesman said: "The PSNI has a legal responsibility for the care and management of all information that it holds - this is a responsibility which must be taken extremely seriously. At the same time, the PSNI also recognises the statutory responsibility to provide information to the Police Ombudsman, enabling exercise of his functions and legal responsibilities.
"Police are currently seeking to agree a solution with PONI around these complicated, and sometimes unfortunately competing, legal issues."
The spokesman added: "Until we can get a resolution, PSNI believes that it has responded appropriately to each request, giving careful consideration on a case by case basis, to ensure that the respective legal requirements are met.
"PSNI will continue to work with PONI to seek to get an agreement over our respective obligations and ensure we both have shared understanding of the legal framework."
A Policing Board spokesman said the application for a judicial review was "very significant and a matter of great concern".
The issue will be discussed with the PSNI Chief Constable at a meeting of the board this week.
Police cooperation and the provision of information to the institutions with legislative responsibility for delivering independent oversight and accountability of the PSNI is critical.
Sinn Féin Policing Board member Caitríona Ruane said: "This is affecting several key and high profile cases in which families, such as those in Loughinisland, are seeking the truth and will damage overall confidence in the PSNI.
"It is therefore not surprising that the Ombudsman has been forced to take this action against Matt Baggott.
"We commend him for exhausting every avenue to conclude on these investigations despite the barriers being put in place and support victims and survivors and their families."
SDLP leader Alasdair McDonnell expressed disappointment that legal action was "the only option".
He said: "Such a level of obstruction is appalling and only serves to prolong the heartache of grieving families who deserve to know the truth about the deaths of their loved ones.
"The peace process will never be complete satisfactorily until the truth, and the whole truth, is established. However, the Ombudsman's office must be allowed to do its job and, therefore, it is essential."