李國能在聲明就立法對司法機構的兩點影響評論，第一是法工委文件中提及由特首指定法官審理國安法案件，他認為做法損害司法獨立（detrimental to the independence of the Judiciary）。
第二點是，法工委說明文件提到中央機構或對「極少數」危害國家安全犯罪案件行使管轄權，李國能指，這惹起極大憂慮。他認為，中央機構一旦行使管轄權，有關案件將在內地處理及審理，被告將不享用香港司法程序的保障；即使中央只會在「極少數」行使管轄權，仍然破壞《基本法》下香港法院獲授權行使的獨立司法權力（would undermine the independent judicial power which our courts are authorized to exercise under the Basic Law.）。
全國人大會議 6 月初通過制定「港區國安法」的決定草案，李國能當時撰文回應，指特區政府就基本法23條立法無期，認為人大為香港立國安法是「可以理解及合理的」。但他稱，實際立法內容必須與普通法原則一致，他提出7項建議，包括法例不具追溯力、罪行定義必須合理確切、在港公開公正審訊、調查權力須受香港法律規管、搜查處所及監聽電話須獲得司法授權。對於當時有建議禁止外國護照法官處理國安相關案件，李國能回應指，這項建議有損基本法保障的司法獨立原則。
It is unfortunate that the draft law has not yet been published. But it is significant to note that the Explanation of the Legislative Affairs Commission of the NPCSC had stated that the legal principles of our system would be followed, including the presumption of innocence. There is no suggestion that the law would be retrospective.
I wish to comment on two matters affecting the Judiciary.
First, it was stated that the Chief Executive would have the power to select the judges who would deal with national security cases. This would be detrimental to the independence of the Judiciary.
Under the Basic Law, judges are appointed by the Chief Executive (CE) on the recommendation of an independent commission, that is, the Judicial Officers Recommendation Commission. Judges are chosen on the basis of their judicial and professional qualities and exercise their judicial power independently free from any interference.
The Judiciary is independent from the executive authorities. It is the independent Judiciary which should decide on the judges who would hear these cases without any interference from the executive authorities.
Further, the CE would not have the required knowledge of the experience and expertise of the judges to make the selection on his or her own. And the CE's chairmanship of the National Security Commission to be established in Hong Kong would make it inappropriate for the CE to make the choice on his or her own.
If this view is not acceptable, then the arrangement should at least provide that the CE's selection of these judges must be based on the recommendation of the Chief Justice or that of the Judicial Officers Recommendation Commission. This would ensure that the choice will be made on a professional and independent basis.
Secondly, the Explanation stated that under specific circumstances, the central authorities may exercise jurisdiction over a tiny number of criminal cases that jeopardise national security. This also raises serious concern.
When exercised, these cases will be dealt with and tried in the Mainland. The defendant would not enjoy the safeguards of our judicial process. Although this jurisdiction could only be exercised in the most exceptional circumstances, it would undermine the independent judicial power which our courts are authorized to exercise under the Basic Law.