The warning by General Vladimir Padrino Lopez, who is also Maduro's defense minister, came after more than two months of violent clashes between protesters and security forces.
The opposition and a press rights group say security forces have attacked, robbed and run over protesters and journalists.
Fresh clashes erupted on Wednesday, as thousands of protesters tried to March to the offices of the electoral authority from various points of the capital.
Related reading
Up to 200,000 protesters march against Venezuela's Maduro
A 17-year-old boy was killed during a march in the Chacao district in eastern Caracas, taking the overall death toll since the beginning of April to 66, according to prosecutors.
The circumstances of the boy's death was being investigated, the public ministry said. Opposition leaders said security forces were to blame. On Monday, videos published on social media had appeared to show security forces attacking and robbing people of their belongings.
"I do not want to see any more guards committing atrocities in the street," Padrino said in a public address on Tuesday.
"Whoever departs from state policy, which gives pre-eminence to respect for human rights, and who acts unprofessionally, will have to answer for it."
The opposition-controlled legislature has accused Interior Minister, Nestor Reverol of being responsible for the "repression" of protesters.
Reverol has been hit by US sanctions for alleged involvement in drug-trafficking. Maduro's opponents are protesting to demand early elections to remove him from power. They blame him for a desperate economic crisis.
"We have to stay in the street until Maduro negotiates his departure or the military withdraws its support for him," senior opposition lawmaker Freddy Guevara said on Wednesday.
Maduro says the crisis is a US-backed conspiracy and brands the protesters insurgents and terrorists.
