Artificial intelligence systems can expand the capabilities and enhance the efficiency of law enforcement agencies preventing, investigating, detecting, and prosecuting criminal offences in the European Union. At the same time, the deployment of artificial intelligence in the security domain often raises numerous legal and ethical concerns. The ALIGNER Fundamental Rights Impact Assessment is an operational tool, rooted in fundamental rights and in the principles of AI ethics, ready to be integrated in the AI governance measures of European law enforcement agencies to inform their decision-making processes and ensure compliance with the recently adopted Artificial Intelligence Act. This paper first introduces the main tensions between law enforcement AI and fundamental rights, as enshrined in the Charter of Fundamental Rights of the European Union; then, it gives an overview of the main developments and best practices in AI governance and their relationship with fundamental rights as well as AI ethics; and finally, it describes the structure of the ALIGNER Fundamental Rights Impact Assessment.