VILNIUS, U.S.S.R., JAN. 27 -- A Soviet army officer shot and wounded a Lithuanian motorist at a military checkpoint here today -- apparently accidentally -- and officials of this secessionist Baltic republic said they have begun keeping a detailed record of Soviet abuse of local citizens.

Government spokesman Audrius Azubalis said a Soviet army patrol stopped the motorist -- who was driving a car also occupied by two hitchhikers -- and asked him to get out of the car and put his hands on the windshield.

As the motorist moved to comply, authorities said, a shot fired at the ground by an army captain, apparently as a warning, ricocheted and hit the man in the leg. The victim was taken to a Vilnius hospital for treatment.

Azubalis said also that the last one of six Lithuanians seized by the Soviet military after a shooting incident involving troops last Thursday had been released and was being treated at a hospital for a concussion.

Troops have been patrolling major Lithuanian cities and highways since a weekend of army violence in Vilnius two weeks ago claimed the lives of 13 civilians. Azubalis said the Lithuanian government is now formally logging complaints against Soviet troops and police and that local authorites had agreed with Soviet prosecutors to work on a joint investigation of all such incidents.