Two senior Saudi princes who claimed sovereign immunity to avoid a court case involving their business interests cannot exempt themselves from English justice, the high court has ruled.

Neither Prince Mishal bin Abdulaziz Al Saud, a former defence minister and brother of King Abdullah and chairman of the country's influential allegiance council, nor his son Prince Abdulaziz bin Mishal bin Al Saud are members of the Saudi royal household, Mr Justice Vos said.

His 40-page decision was a setback for the princes, whose lawyers had based some of their arguments on the fact that they receive special treatment from UK border staff and do not pass through immigration controls when entering Britain.

There are an estimated 5,000 princes in the ruling Al Saud family in Saudi Arabia. A victory for Bin Mishal and Bin Abdulaziz would have had far reaching implications for others holding that status.

The high court judgment could aggravate tensions in relations between Britain and Saudi Arabia, already strained by the changes of the Arab spring. It may undermine the sense in Riyadh that members of the Al Saud dynasty enjoy special privileges abroad as well as at home as a result of their position. Unofficial Saudi sources suggested, however, that the attempt to claim immunity was not appropriate because the case was a commercial one, not a political one.

In a related case, emerging from the same dispute, lawyers for the princes have warned that relations between Saudi Arabia and Britain will suffer if what are said to be highly damaging allegations about business deals surface during court hearings in London.

In his judgment, Vos said membership of a royal household "would be likely to be restricted to the case of a regent, heir to the throne or a person broadly exercising the sovereign's or head of state's function in a full-time capacity on his behalf".

Even if they were to be considered to be part of a royal household, Mr Justice Vos added, "the princes would have no immunity to these proceedings, relating to their alleged commercial activities".

Mohammed bin Nawaf Al Saud, the Saudi ambassador to the UK, explained in a witness statement to the court that Prince Mishal, one of the plaintiffs, is second in line to the Saudi throne by birthright, though the allegiance institution law of 2006 makes clear that succession is not by birth but by the council choosing from three nominees selected by the king.

The dispute involves a company called FI Call Ltd and rival claims over the sale of $6.7m (£4.3m) worth of shares in a case one judge has described as throwing up "a nuclear mushroom cloud" of litigation.

The first petition to the high court initiating the complex case was submitted by Global Torch, the company said to represent the Saudis' interests. A counter petition was then served by their former partner in FI Call, a Jordanian businessman, Faisal Almhairat.

Steven Morris, of the law firm Howard Kennedy FSI, which represents Almhairat, welcomed the judgment. He said: "From the outset of these proceedings, my clients have always had the utmost confidence in, and respect for, the integrity of the English judicial system; that confidence has been vindicated by the Judgment of Mr Justice Vos. It is understood that the two Princes are appealing to the court of appeal."

In his judgment, Mr Justice Vos had also pointed out that "Prince Mishal's story changed significantly" during the course of the case and included the claim that he worked full time undertaking duties duties on behalf of the King.

"I simply cannot accept it at face value," Vos added. "It is flatly inconsistent with the way Prince Mishal originally put his case."

Saudi officials hinted at a review of ties with the UK last autumn when the Commons foreign affairs committee announced an investigation into relations with Bahrain and Saudi Arabia. Its report, due in the spring, is awaited nervously in Whitehall.

David Cameron was criticised by anti-arms sales campaigners for a trip to Saudi Arabia last November to help secure a £7bn fighter aircraft and equipment deal with BAE Systems.

It followed an extraordinary outburst by the Saudi ambassador, who said the kingdom felt "insulted" by the parliamentary investigation.

In 2008 the Saudis pressured Tony Blair's government to shut down a criminal investigation into billions of dollars in allegedly improper payments made by BAE to obtain Saudi contracts. The British ambassador to Saudi Arabia warned that counter-terrorism cooperation could be damaged iof the probe continued. There was criticism at the time that the true motivation for shelving the case was to protect UK commercial interests.

Prince Bandar bin Sultan, the former Saudi ambassador to the US and now the country's intelligence chief, was allegedly the prime recipient of the improper payments.

The Guardian is seeking access to documents in the case detailing disputed transactions involving Saudi interests in Beirut and Nairobi. At an earlier hearing another judge ordered that they should be released in principle. They are being withheld pending an appeal against that decision by lawyers for the Saudis to the appeal court.

The case continues.