Senior UK special forces officers had suspicions of a "deliberate policy" of murder by the Special Air Service (SAS) in Afghanistan but hid evidence, an inquiry heard.
In some cases, they did nothing and in others "sought to prevent adequate investigation," a lawyer for families of those killed said.
Internal emails show "incredulity" at official reports of SAS night raids in which Afghans were killed, he said.
Concerns of SAS wrongdoing were widely known at the top of government.
On the third day of the independent inquiry, the Ministry of Defense (MoD) was accused of misleading the High Court.
The probe was launched following a BBC Panorama investigation, which revealed that a SAS squadron killed 54 people in suspicious circumstances on one six-month tour.
The inquiry is seeking to establish if UK special forces carried out executions during operations in Afghanistan between 2010 and 2013, as well as examining the alleged cover-up of illegal activity and inadequate investigations by the military police.
Emails released as part of the inquiry revealed the head of the MoD's legal department discussed the "highly questionable, if not actually implausible" justifications the SAS had given for killing dozens of people in southern Afghanistan, including children.
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