El Salvador holds people accused of violating the mandatory home quarantine decreed by President Nayib Bukele in March even though the Supreme Court has since ordered him to not detain such people.
People in a sports center in the capital, San Salvador, said they had been in quarantine for more than 40 days; they also said they had been tested but did not get the results.
The Salvadoran government did not immediately respond to a Reuters request for comment.
Pablo Perez, a 52-year-old farmer, who said he was detained for walking in the street, said people at the center were in good health. He added that people there were regularly checked by doctors.
Meanwhile, in a center set up in a parking lot of a Baptist church in the capital, another group of people took to the windows and terraces to denounce overcrowding, inadequate conditions and the lack of test results.
Riot police guarded the protests, Reuters witnesses said.
Last week, rights groups condemned Bukele after he released startling photos of hundreds of jailed gang members stripped to underwear and pressed together in formation, part of a punishment for an outbreak of violence.
El Salvador, which has reported 13 deaths and 555 confirmed cases, has 91 containment centers; 3,964 people are quarantined there, according to an official data.