It was originally reported that the allegations were made against one soldier from The Argyll and Sutherland Highlanders, 5th Battalion, The Royal Regiment of Scotland, but it emerged from a freedom of information request that the investigation surrounded three individuals.
The Ministry of Defence (MoD) said an independent investigation found that no further action should be pursued due to insufficient evidence.
The allegations centred on the Scottish battalion's tour of duty in Afghanistan between September 2010 and April 2011, as part of Operation Herrick 13, and included claims that fingers of members of the Taliban were collected and kept as "trophies".
The case was referred to the independent Service Prosecuting Authority, which investigated the three service personnel for the offence of "outrages upon personal dignity", under the War Crimes section (Article 8) of the International Criminal Court Act 2001, (Elements of Crime) Regulations 2004.
In response to a request for information, the MoD said: "After consideration, the director of Service Prosecutions directed that no charges should be brought against any of the three individuals, due to insufficient evidence."
The MoD said "internal administrative action" was also considered against the three individuals but the information relating to this was not released because it is protected by the principles of the Data Protection Act 1998.