Relations between the UK and Saudi Arabia will suffer if what are said to be highly damaging allegations about business deals surface during a London trial, lawyers for two Saudi princes have warned the high court.

The resort to political justifications – among other reasons – for suppressing the disputed claims is revealed in a ruling delivered on Wednesday by Mr Justice Morgan. The judgment upholds, in principle, requests by the Guardian and Financial Times to be given documents detailing the disputed transactions involving Saudi interests in Beirut and Nairobi.

The allegations are said to be so serious that if published they would upset relations not only between the oil-rich kingdom and the UK but also have an "adverse effect" on Saudi links with the US. The Saudis have dismissed them as untrue, "outrageous" and "scandalous".

The companies court judge has given the Saudis time to appeal against his decision. A confidential annex to the judgment is, therefore, not yet being made public; it remains temporarily closed pending an appeal.

The dispute, which has erupted over the sale of $6.7m (£4.3m) worth of shares, has "thrown up a nuclear mushroom cloud" of litigation, Mr Justice Morgan said.

Lawyers for Prince Mishal bin Abdul Aziz Al Saud, his son, Prince Abdulaziz, and others have indicated they will go to the court of appeal to challenge the decision and prevent details of the allegations being released.

Prince Mishal, 86, is a former defence minister and currently chairman of the influential Allegiance Council, which determines succession to the Saudi throne. He is said to be in a frail state of health. The complex case raises issues about whether the transparency of British justice can be upheld in internationally sensitive cases.

A separate hearing, relating to the same raft of litigation, has explored how far the legal doctrine of sovereign immunity could extend into the Saudi royal family, which has thousands of members, so as to protect them from being sued in the UK. The case comes at a time when Russian oligarchs, Middle East businessmen and Asian corporations are increasingly turning to the London courts to resolve legal disputes.

The claims have erupted from a bitter disagreement with a Jordanian businessman, Faisal Almhairat, once the Saudis' partner in a firm called FI Call Ltd. At one stage, it is alleged, Prince Abdulaziz complained to the Saudi authorities which led "to the issue of an arrest warrant against Mr Almhairat and the involvement of Interpol in Saudi Arabia and Jordan".

The lawyers for Prince Mishal, Prince Abdulaziz, and others have told the court that the allegations are false, "scandalous and outrageous", according to the judgment. They were made, it was said, "in order to put pressure on the Global Torch parties 'through the fear of publicity'". The aim was to cause "reputational damage, embarrassment and distress".

The lawyers for Global Torch Ltd, the company said to represent the Saudis' interests, argued that aspects of the business trial should "not be aired in open court" because the allegations are "wholly false".

A solicitor acting for Global Torch told the court, according the judgment, that "publicity for the [Beirut transaction] allegation" would result in Prince Abdulaziz and Emad Ayshih, a director of FI Call Ltd, being at risk of "serious personal injury or death from reprisals from citizens of Saudi Arabia or certain organisations".

The solicitor also said that: "The two princes would be associated with the kingdom of Saudi Arabia and the allegations would lead to an adverse effect on relations between the US and Saudi Arabia.

"Further, Saudi Arabia would regard the United Kingdom with suspicion in so far as the courts of the United Kingdom had permitted these allegations to be made public in court proceedings."

Such warnings from senior Saudis are not unprecedented. In 2006 the Saudis threatened to end counter-terrorist co-operation with the UK unless the Serious Fraud Office dropped its investigation into BAE Systems over the al-Yamamah arms deal. It resulted in the investigation being shelved.

Almhairat denies any wrongdoing and says he has not sought publicity to put pressure on Global Torch. His counsel, Robert Howe QC, said he was simply "an individual who had found himself in a large commercial dispute concerning with some very rich and powerful men".

Guy Vassall-Adams, counsel for the Guardian and FT, told the companies court that the allegations "were serious and raised matters of widespread national and international concern". The allegations in the documents related to matters of "the highest public interest". Privilege to report them would depend on the coverage being "fair and accurate".

Morgan's judgment, which examines the limits of secret justice, reinforces the principle that papers attached to a court case should be available to the media and public. "The documents sought … are sought for proper journalistic reason," Morgan explained.

"There is likely to be considerable interest in the material contained. There are good reasons why the news media should have available to them the documents which they seek to assist them in preparing a fair and accurate report of hearings which have, or should have, taken place in public."

In terms of the Saudis' privacy application, the judge said: "The fact that a hearing in open court may be painful, humiliating and a deterrent either to a party or a witness is not normally a proper basis for departing from the open justice principle.

"The court hearings in this litigation should take place in open court unless there later emerges some new material which would justify a different approach."

A "confidential schedule" containing five allegations against Global Torch should therefore be made public, the judge said, if the ruling is "left unreversed by an appellate court".