The News of the World has suspended its news editor Ian Edmondson over allegations of phone-hacking at the paper in 2005-06.
A spokesman for the newspaper said an individual had been suspended following "a serious allegation" of wrongdoing.
The BBC understands these relate to allegations made by actress Sienna Miller that her phone was hacked.
The paper's former royal editor was jailed in 2007 for conspiracy to access phone messages.
Clive Goodman had intercepted voicemails left for royal aides. Private investigator Glenn Mulcaire was jailed for six months on the same charge.
The paper's then editor Andy Coulson resigned - despite saying he had not been aware of what was going on - and is now Prime Minister David Cameron's director of communications.
The News of the World said the case was a one-off, but former employees have subsequently claimed the practice was widespread, and some of those who say they were targeted, including Labour politicians, have called for Mr Coulson to be sacked.
Despite this, Mr Coulson has received strong backing from No 10.
A spokesman said the latest allegation was the subject of legal action as well as an internal investigation and, if proven, "appropriate action" would be taken.
"The News of the World has a zero tolerance approach to any wrong-doing," he added.
Mr Edmondson's official title is Assistant Editor (news) and until just before Christmas, he worked under the overall editor of the paper Colin Myler.
Miss Miller is one of a number of people currently taking action through the courts claiming that their privacy was breached by the News of the World.
The BBC's Jon Manel says he has seen court papers relating to her case which reference notebooks belonging to Mulcaire.
He says the legal document claims some pages of the notebooks have the name "Ian" in the top left hand corner, and goes on to say that the claimant, Ms Miller, infers that to be Mr Edmondson.
Our correspondent says the High Court has also ordered Mulcaire to answer a series of questions about another case, brought by a woman called Nicola Philips, who used to work with the publicist Max Clifford.
One of those questions is: "Did Ian Edmondson request him to investigate the claimant?"
Mulcaire is understood to be appealing against that order.
The News of the World is the UK's biggest selling Sunday newspaper, selling more than 2.7 million copies each week on average in November.