Lord Justice Coghlin said on Tuesday that public confidence in those in power may diminish with any continuing delay in publishing information on terminations.
His caution came as the Department of Health won an appeal against an order for discovery of all documents relevant to the case.
The Court of Appeal ruled that the material should instead be inspected first by the judge, who is due to hear the judicial review challenge later this month.
The Family Planning Association (FPA) issued proceedings against the Department over the continued non-publication of guidelines.
The sexual health charity claims there was a legitimate expectation that revised guidance would be completed following earlier court orders.
Under current law, abortion is illegal in Northern Ireland - except in limited circumstances where the mother's life or mental well-being are considered at risk.
In 2009, the Department published a document which, for the first time, provided guidance to health professionals in Northern Ireland on terminating pregnancy.
But later that year, the High Court ruled that it did not properly cover counselling and conscientious objection issues.
A judge held that the guidelines were misleading and should be withdrawn for reconsideration.
Since then, a fresh public consultation process on counselling and conscientious objection has been undertaken as part of the redrafting.
It seems to me the danger is in the Department taking a view: 'No, you can't see these documents' - despite the fact it has taken so long to consider what we should do.
Lord Justice Coghlin
Appearing before a three-judge Court of Appeal panel on Tuesday, on behalf of the Department and Health Minister Edwin Poots, Attorney General John Larkin QC contended there was nothing in the documents that assists the FPA's case.
He confirmed, however, that he was happy for the court to study the material, which Mr Poots has been considering, and form its own view.
During the hearing, it was noted that departmental guidance has been awaited since a ruling in 2004.
Lord Justice Coghlin, sitting with Lord Chief Justice Morgan and Lord Justice Girvan, said: "There comes a stage in any government activity when delay becomes much more than simply ... the government going ahead with its work, and it becomes a matter of real concern to the governed.
"It can be interpreted by the governed, not so much the diligent work of government, but as a paralysed government that - because of its cultural and religious divisions - simply cannot bring itself to discharge its duties.
"That's why there is a duty of candour."
Mr Larkin stressed, however, that Northern Ireland's constitutional arrangements must be acknowledged.
He also pointed out that Mr Poots only became Health Minister in 2011 and has been working continuously with officials to comply with the requirement to publish guidance.
According to the Attorney General, the FPA has been premature in mounting a challenge to emerging public policy.
"We are in a fluid state, in terms of the development of government policy," he said.
Lord Justice Coghlin told him: "Nobody is denying for a minute that it's a finely balanced judgment.
"But the longer time goes on, the less trust the governed may have in the government."
Tony McGleenan QC, for the FPA, argued that the delay has been "unconscionable".
He claimed there could come a point, not yet reached, when it would amount to an abuse of power.
Following the court's ruling, the judge in the judicial review hearing will now decide the merits of the material sought.
Lord Chief Justice Morgan confirmed: "He should inspect the documents with a view to determining whether, after such inspection, the documents should be provided on the basis of the legal test."