Some 12 police officers and a dozens civilians were injured as protesters set on fire toll booths near Kalimash tunnel on the Milot-Morine highway linking the country with Kosovo, images from Report TV showed.
On Sunday, the police arrested 23 inhabitants of the northern town of Kukes suspected of violent disorder during the protest.
Later in the day prime minister Edi Rama condemned the violence but said lower taxes will be applied for frequent users and for the socially disadvantaged living in the area.
The toll fees range from 2.5 euro for a motorcycle, 5 euro for cars to 22.5 euro for heavy trucks.
They have been criticised as excessively high by Kosovo citizens and government officials, as well, including by prime minister Ramush Haradinaj.
In 2016, the Albanian government signed a 30-year concession contract with a consortium comprising Abu Dhabi-based Catalyst Viva Das General Contracting and Albanian companies LLC, Salillari, Bee Tech, Violiap Ateve, Kastrati for the maintenance of Milot-Morine highway.