The second incident was reportedly with a 50-year-old woman in the politician's Hull constituency. Her family declined to comment yesterday. However, this relationship, even if confirmed, may not constitute misconduct.
Close protection officer Pc Paul Rice guarded Mr Johnson when he was Home Secretary. An internal police inquiry will now look into both alleged relationships, it is understood.
The protection officer is also thought to have worked for Theresa May since she took over at the Home Office last May.
Mr Johnson quit Labour's frontbench last Thursday, forcing leader Ed Miliband to reshuffle his Cabinet.
In a statement the following day, Scotland Yard said: "A Metropolitan Police Service (MPS) Specialist Operations Police Constable has today, Friday, January 21, been suspended from duty pending the outcome of the Directorate of Professional Standards (DPS) investigation into allegations reported in the media regarding an inappropriate relationship.
"The matter was referred by the MPS Specialist Operations Unit to the DPS on January 20. A thorough investigation is now under way. As the allegation is subject to investigation, we are not able to comment further at this stage."
Mr Johnson has refused to elaborate on the "personal reasons" for his shock resignation, saying only that he was finding it "difficult to cope" with "personal issues in my private life". He has been married to Laura, his second wife, for almost 20 years, and the couple have a 10-year-old son.
Although many Labour supporters are concerned at the loss of such a popular figure from the party's frontbench, it has been made clear Mr Johnson will not be stepping down from the Hull West and Hessle seat he has held since 1997.
His constituency agent, Stuart Spandler, said yesterday: "We had a meeting on Thursday night and he told us he was carrying on as MP. His job is carrying on with his constituency and Parliamentary duties, that's all I can really tell you. I haven't discussed any of the personal details at all with him; that's his private life and that's nothing to do with me as his agent."
Mr Johnson has been replaced as Shadow Chancellor by Morley and Outwood MP Ed Balls, who was overlooked for the post last October after disagreeing with Mr Miliband over economic policy during Labour's leadership campaign.
Shadow Foreign Secretary Douglas Alexander has admitted the loss of "as significant a figure as" Mr Johnson from the frontbench was a blow to Labour.
But, he added: "There is a new team in place. Ed has made his decision in terms of the personnel and I think we are determined to pull together, leave behind some of the problems of the past and start anticipating some of the questions that Labour needs to be answering that people will be asking us over the next three, four or five years."
Labour's Deputy Leader Harriet Harman insisted the Shadow Cabinet was united behind its economic policy and said Mr Balls and Mr Miliband were in "strong agreement".
She said: "We are all agreed on this, that the line of argument was established following on from what Alistair Darling did while in Government. The line was established by Ed Miliband and Alan Johnson and that is the line we are taking forward with Ed Balls as Shadow Chancellor after Alan Johnson's very sad resignation."
Speaking about Mr Johnson's resignation, she said: "I am very disappointed indeed that he has felt that he needed to resign because I think that is a loss not just to the Labour Party but to frontline politics."