Tony Blair raised fears about an investigation into a Saudi arms deal days before it was dropped last year, a newly-disclosed document has shown.
Critics said the corruption probe threatened a major Eurofighter deal
The then PM had said the decision to stop the probe into the BAE deal was taken because of national security and was not linked to commercial interests.
But in a letter released during a legal case, Mr Blair refers to "concern" over ongoing business negotiations.
Downing Street has refused to comment on the letter to his attorney general.
The letter from Mr Blair to Lord Goldsmith dated 8 December 2006 was released to the High Court during a case brought by two pressure groups who are challenging the legality of the decision to end investigations into BAE Systems' dealings with Saudi Arabia.
It refers "critical difficulties" that might have affected the major contract for new military aircraft.
There was uproar when the Serious Fraud Office inquiry into the Al Yamamah contract from the 1980s was dropped, but Mr Blair insisted the decision was taken on security grounds.
BAE, the UK's largest defence group, and the Saudis have always said they acted lawfully.
Six days after the letter was written, Lord Goldsmith announced to the House of Lords that the probe into allegations of kickbacks to Saudi princes was being suspended.
He said diplomatic cooperation between Britain and Saudi Arabia was being put at risk by the investigation, with implications for UK security.
Recent reports have suggested that Saudi Arabia had threatened to pull out of a potential new order for Typhoons.
In the letter to Lord Goldsmith, Mr Blair acknowledged that his intervention in such a case was unusual but said he would be failing in his duty if he did not point out the security issues at stake.
He went on to say: "While this letter is not primarily concerned with the serious damage being done to our bilateral relationship by the investigation, it is of course of concern to me, not least because of the critical difficulties present to the negotiations over the Typhoon contract."
In September, the Ministry of Defence announced a £4.43bn deal to sell 72 Typhoon aircraft to Saudi Arabia in September.
The contract safeguarded thousands of jobs in the north-west, where the planes will be partly built by BAE Systems.