The moment featured Captain Jack (John Barrowman) sleeping with a barman and is expected to be shown in the US on cable network Starz, The Sun reports.
However, the scene will be cut from the UK broadcast as it was allegedly deemed inappropriate for a primetime slot on BBC One.
"It wasn't that it was a gay scene that worried people, but just the fact that it was such an explicit sex scene full stop," a source said. "You can get away with scenes like that on American cable channels, but you can't on primetime BBC One.
"Even though the show airs after the watershed, it has a lot of young fans who would have been shocked at the graphic nature of the sex."
A BBC spokesperson confirmed that the scene will not be shown in the UK, adding that a violent moment will also be cut later in the series.
"The UK and US versions of Torchwood are slightly different," the spokesperson said. "However, these differences do not change the story in any way and the strong storylines are first and foremost to the series."
Barrowman, who has previously said that Jack has "full-on boy sex" in the show, recently admitted that he would like to make a Torchwood movie.
Torchwood: Miracle Day airs on Fridays at 10pm on Starz in the US and on Thursdays at 9pm on BBC One in the UK.
Watch John Barrowman discussing Torchwood: Miracle Day with Digital Spy below: