This was the second protest in weeks by Bolivian doctors
The doctors, whose protest included offering free treatment themselves, say the Cubans take jobs away from unemployed Bolivian doctors.
They want the Bolivian government to subsidise the national medical service, so it is free at the point of delivery.
But the Bolivian President Evo Morales has accused the doctors of selfishness.
Over 1,000 doctors are reported to have been dispatched by Cuba to provide health services in Bolivia, along with several thousand in Venezuela.
Cuba has reportedly equipped some 20 Bolivian hospitals and is behind Operation Miracle, a drive to operate on the eyes of 14,000 Bolivians with cataracts.
Thursday's protest was the second organised by doctors from the Medical College of La Paz.
The college president Eduardo Chavez, a driving force behind both protests, said "a fundamental social pillar such as the health of a people" should not be left in the hands of foreigners.
He complained that Bolivian doctors were not being given opportunities to join the ranks of the Cuban doctors working in poor, undeveloped areas of Bolivia - one of the poorest countries in the world.
And he said the recently elected government of Mr Morales should focus their efforts on providing healthcare free at the point of delivery.
The protest comes amid growing criticism by opposition politicians of what they say is the influence of the Cuban government in Bolivia.
But Mr Morales has accused the doctors of acting selfishly and against the interests of Bolivia's most disadvantaged people.
Deputy Health Minister Juan Alberto Nogales said Bolivia's health indices were among "the worst in Latin America, if not the world", and were a permanent preoccupation for the government, according to the news agency Efe.
"In those places where we are supporting our Cuban colleagues there has never been a medical service," he said, rejecting the doctors' assertion that the Cubans were taking away jobs.
BBC NEWS | Americas | Bolivia protest over Cuba medics