In Lima, the capital, riot police fired tear gas at several hundred student protesters, some of whom threw rocks and petrol bombs.
In Peru's second largest city, Arequipa, demonstrators burnt a blood-smeared effigy of Alan Garcia, the Peruvian president, who backed the laws as part of the free trade deal with the US.
Violence reached its peak last Friday when police opened fire as they tried to break through a highway blockade manned by thousands of protesters.
At least 22 police offers were killed during the clashes.
Repercussions from the violence have also rocked the government, with Carmen Vildoso, the women's affairs minister, resigning on Monday in protest over the government's crackdown.
Opposition parties also continued calls on Thursday for Yehuda Simon, the prime minister, to stand down over the crisis.
On Wednesday, Nicaragua granted political asylum to a protest leader charged with sedition after the protests.
Alberto Pizango had accused the Peruvian government of "genocide" following Friday's clashes.
Peru's indigenous peoples say that Garcia's government did not consult them in good faith before signing contracts that could affect at least 30,000 of them across six provinces.