The Scottish Government has insisted ministers would only give a directive to the police authority as a “last resort.”
A spokeswoman said they would never “directly interfere” with operational policing.
She added that the Scottish Police Authority (SPA) was independent and established to hold Chief Constable Sir Stephen House to account.
The spokeswoman said: “In a democracy, it is fundamental that the cabinet secretary for justice and the government should not direct the police.
“The act is unequivocally clear that Scottish ministers cannot direct the police in relation to any specific operational activity.
“The Police and Fire Reform (Scotland) Act 2012 is also very clear that the SPA and chief constable must have regard to any report produced by the HMICS and must take such measures as they think fit to address the recommendations within the report.
“Powers of ministerial direction to direct the SPA to take measures following HMICS recommendations would only be used as a last resort- they would never directly interfere in operational policing.”
But Highland Council deputy leader David Alston accused the justice secretary of “shirking responsibility” for the row because it was now clear the issue was a policy matter.
Highland MSP John Finnie, who is opposed to the firearms policy, said he hoped Police Scotland would enact all recommendation put forward by HM Inspector of Constabulary in Scotland.
Highland Labour MSP Dave Stewart said he could envisage the possibility of Kenny MacAskill being forced to issue a ministerial directive to the SPA.