Tuesday's warning by General Vladimir Padrino Lopez, who is also President Nicolas 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 run over, attacked and robbed protesters and journalists.
Videos published on social media on Monday appeared to show security forces 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.
"Whoever departs from state policy, which gives preeminence to respect for human rights, and who acts unprofessionally, will have to answer for it."
Prosecutors say 65 people have been killed in the unrest since April 1.
Maduro's opponents are protesting to demand early elections to remove him from power.
They blame him for a desperate economic crisis and accuse him of clinging to power and repressing demonstrators.
He says the crisis is a US-backed conspiracy.
Opposition leaders called on their supporters to head for the offices of the electoral authority on Wednesday in the latest protest.
"We will see who is really in charge of the armed forces," said opposition congressional speaker Julio Borges.
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