The Prime Minister reportedly asked Lord Udny-Lister – a Middle East expert and a long-standing aide dating back to his days as London mayor – to look into the complaint.
Lord Udny-Lister was said to have responded by saying that he would “investigate”.
The Saudis finally withdrew from the deal last July – blaming the Premier League for its collapse – to the anger of many Newcastle fans who believed their investment could revitalise the club’s fortunes.
The report comes after Mr Johnson this week ordered a review into the collapse of the financial firm Greensill Capital amid concern over David Cameron’s lobbying on its behalf.
The former prime minister has faced criticism that his actions included lobbying Mohammed bin Salman at a time when he was implicated in the murder of the Saudi journalist Jamal Khashoggi.
In response to the Mail report, a Government spokesman said: “While we welcome overseas investment, this was a commercial matter for the parties concerned and the Government was not involved at any point in the takeover talks on the sale of Newcastle United.”
According to the Mail, the crown prince sent a message to Mr Johnson last June after he was angered by a demand from the Premier League to know whether the proposed deal would mean the club would be owned by the Saudi state.
“We expect the English Premier League to reconsider and correct its wrong conclusion,” the prince is said to have warned.
In a message to his private office, Mr Johnson said “One for Sir Edward” – a reference to Lord Udny-Lister, who at the time had not yet been installed in the House of Lords.
Lord Udny-Lister reportedly told the Prime Minister: “I’m on the case. I will investigate.”
Lord Udny-Lister told the Mail: “The Saudis were getting upset. We were not lobbying for them to buy it or not to buy it. We wanted them (the Premier League) to be straightforward and say ‘yes’ or ‘no’, don’t leave them (the Saudis) dangling.”