Hundreds of people contacted the BBC to complain that the music on the BBC Two programme was drowning out Cox's commentary on the formation of the universe.
Writing on a BBC discussion forum, one viewer said: "Yet again a programme we have been looking forward to utterly ruined by music that drowns out the words. Why does the BBC think its viewers need to have every second filled with noise? We haven't got the attention span of a gnat."
Another added: "Surely it is within the bounds of 21st century technology to put this 'music' or background noise on the same basis as subtitles? In other words, like subtitles, give the viewer the option of turning it on or off."
As a result of the complaints, the Wonders of the Universe production team has agreed to turn down the volume of the background music.
Jonathan Renouf, the show's executive producer, said: "Clearly none of us set out to make programmes where we can't hear the presenter, so if we have got that wrong then we need to do something about it. There's been enough volume of complaints (sic) about this that I think we clearly have made an error of judgment.
"So we are remixing the sound for all the films to pull down the music and effects levels during the segments where Brian is talking, and we are very hopeful that will correct any problems that the audience have had."
Speaking to The Daily Telegraph, a spokesman for The Royal National Institute for the Deaf said that broadcasters must be more careful when using loud background music.
"This is probably the thing that incenses our members the most. A lot of people have hearing loss in just one ear and for them it's difficult to differentiate between different sounds. Loud background music affects their ability to hear," he said.
"We have talked to a lot of programme makers about this and it is worst in news and factual programmes. Wonders of the Universe is so dramatic anyway, you don't really need the soundtrack."
The spokesman added: "All broadcasters are equally guilty but public service broadcasters should have an obligation to change this."