The Independent Commission of Investigations (INDECOM) is seeking to have one of the judges who heard a constitutional motion brought against it by the Jamaica Defence Force (JDF) recuse herself from writing the judgement in the case.
INDECOM says it has taken action on the basis that the judge is married to the lawyer representing the JDF in a similar matter.
The application is to be heard on Thursday in the Supreme Court.
Justice Carol Lawrence Beswick is one of three judges who more than two years ago heard the case in which the JDF is seeking to stop INDECOM's investigation of the use of mortars during the May 2010 West Kingston security operations.
The judgement is pending.
Her husband, Paul Beswick, last month represented the JDF in the Keith Clarke case in which three soldiers are accused of murder.
In both cases, the issue of immunity has been raised based on certificates signed by the National Security Minister.
Speaking on RJR's call-in programme, Hotline, on Monday afternoon, INDECOM Commissioner Terrence Williams said he believes the situation presents the possibility of a perception of bias.
"A pretty settled principle of law is to make justice appear to be done...to give an appearance which the public will say 'yes, that is a fair hearing of the matter'. So because of what has arisen, we thought it was our duty to make our views be known," Mr Williams argued.
Hearing of arguments in relation to the use of mortars was concluded by the Judicial Review Court in April 2016.
The issue of immunity from prosecution for JDF soldiers only came up in the Keith Clarke case this year and it is set to be heard by the Judicial Review Court.
However, Mr. Williams believes it is important Justice Lawrence Beswick withdraw from the mortar case as it has implications for the Keith Clarke matter.
"What is being relied on now in the Keith Clarke matter is an understanding of the minister's power under the Emergency Powers Act which has not been adjudicated before in Jamaica and will be adjudicated in our matter hopefully for the first time, and so what is being created here is that the precedent to support the appplication in the Keith Clarke matter can come from this other matter which is now pending," he contended.
The INDECOM has also blamed the slow court system for the current situation.