Lawyers for the oversight body also argued that the refusal to hand over sensitive information was irrational and in breach of an agreement drawn up to ensure full co-operation.
The claims were made as Ombudsman Michael Maguire cleared the first stage in his unprecedented legal bid to force the Chief Constable to hand over the material being sought.
But a judge who ruled that an arguable case has been established expressed hope that the impasse will now be resolved away from the courtroom.
The action centres on investigations into recent and historic cases involving allegations of police criminality and misconduct by failing to properly probe murders.
Claims of collusion between some police officers and the killers feature in many.
The Ombudsman claims his requests for information have been turned down on more than 100 occasions.
One of the cases in which the PSNI stands accused of obstructing Mr Maguire's staff is the Loughinisland murders, where loyalist gunmen shot dead six people as they watched the 1994 World Cup in the village bar.
The court heard that access to material is being sought in up to 19 ongoing investigations.
The families of some terrorist murder victims were in court as the case got underway.
They included victims campaigner Raymond McCord, whose son Raymond Jr was beaten to death by a north Belfast loyalist paramilitary gang in 1997.
Barrister Stephen McQuitty, for the Ombudsman, told Mr Justice Treacy proceedings had not been issued lightly.
There's been an unjustified departure from a memorandum of understanding that exists between the police and the Ombudsman.
Barrister Stephen McQuitty, representing the Police Ombudsman
But despite attempts to reach a resolution both sides had conflicting views on the legal requirements.
Arguing that the PSNI was under an obligation to hand over information, he claimed: "The refusal to provide that material is irrational.
"It was contended that the police reasoning was misconceived and mistaken."
Although the document came into operation last September, the court heard that the breakdown in relationships was confirmed in April.
Referring to an affidavit from Adrian McAllister, chief executive in the Police Ombudsman's Office, Mr McQuitty claimed the PSNI began to express concerns about sharing information.
"It was not raised formally but manifests itself in Police Ombudsman staff being turned away from PSNI buildings when they had arranged to view sensitive material," he said.
"It became apparent to the Police Ombudsman that a different approach had been taken."
Senior counsel for the police resisted his move, claiming it was inappropriate and taken with "unseemly haste".
This is a case that would have benefited from, and could still benefit from, engagement between the parties outside hostile, adversarial litigation.
Tony McGleenan QC, for the PSNI Chief Constable
Tony McGleenan QC argued that the Ombudsman has been requesting and receiving sensitive material for years.
But in certain cases the Chief Constable has asked what function is being pursued, he said.
Concerns were also raised over how any information would be handled and shared after being handed over.
An undertaking given by the Police Ombudsman about procedures for ensuring material is stored securely has still to be fully implemented, the court heard.
Urging the judge to adjourn the case to allow further attempts to reach an agreement, Mr McGleenan insisted: "A very large volume of requests by the Police Ombudsman have been responded to by police."
However, Mr Justice Treacy ruled that leave to seek a judicial review should be granted on the basis that the Ombudsman has established an arguable case.
But rather than fixing a date for a full hearing of the challenge, he decided to adjourn for two weeks.
He said: "So far as possible for the court to read the runes that arise from the submissions that have been made, it's quite possible this matter might be resolved between the parties and won't proceed to a substantive hearing.
"One would hope that will happen."