The Police and Border Guard Board has been criticized for deliberately ignoring the rule of law by leaving residence permit applications of Ukrainian citizens unreviewed and imposing arbitrary, burdensome requirements, raising concerns about its adherence to legal principles and the protection of human rights.

On March 19, 2025, the Estonian Police and Border Guard Board announced the rollout of mobile autonomous cameras on patrol cars. These AI-powered devices will automatically record traffic violations using facial recognition and license plate recognition technology, raising significant concerns about privacy, potential misidentification, and the expansion of state surveillance capabilities.

The Estonian Police and Border Guard Board is set to implement a Smart Borders system funded by over €2 million from the European Commission. The system will use advanced surveillance technology — including drones, cameras, radars, and other security equipment — to monitor border traffic and enhance border control measures, an initiative which raises concerns over potential authoritarian surveillance practices.

The Police and Border Guard Board, acting as the lead applicant, joined Lithuania in applying for EU funding to establish a militarized 'drone wall' along the border with Russia and Belarus. The initiative, aimed at enhancing border surveillance and security, was ultimately denied funding by the EU.

The Board has entered a 12‐month contract with surveillance equipment distributor Optimus Systems for advanced security systems along the Estonian-Russian border, with the contract period beginning on October 19. The acquisition raises concerns about increased state surveillance capabilities and potential impacts on civil liberties.

A court ruling on July 27, 2023 found that the Police and Border Guard Board failed to properly assess an international protection claim for a transgender Ukrainian applicant. The court determined that the Board’s procedure was drastically deficient, lacking a cumulative evaluation of the applicant’s gender identity, nationality, and political context, and mandated that the case be re-reviewed with proper legal support.

In March 2023, the Tallinn Administrative Court declared that the forced deportation of a Ukrainian asylum seeker, Roman, by the Police and Border Guard Board was unlawful. The court ordered the agency to compensate him for both material and non-material damages after Roman, pressured during his temporary protection application process, filed a complaint with the help of the Estonian Human Rights Centre.

The Estonian Police and Border Guard Board entered into an agreement with G4S in Estonia to purchase, install, and maintain marine surveillance equipment at a secret location. The technology, which includes radar, cameras, and thermal imaging, will help monitor the sea border for unidentified vessels and potential illegal activities.

Estonia's planned amendment to the State Borders Act would authorize the Police and Border Guard Board to implement pushbacks during mass migration emergencies, potentially breaching international and EU law and raising human rights concerns.