The list of cities with the highest number of infections includes Asuncion, Ciudad del Este that borders Brazil, and Encarnacion near Argentina. The restriction will be in place until April.
Activities related to tourism, contact sports, bars, and restaurants will be limited, and a curfew from 8.00 pm to 5.00 am must be observed.
There will be also a suspension to on-side classes starting Thursday, and work in teams will be mandatory in the public sector. Demonstrations are allowed but only out of curfew hours and in compliance with sanitary measures.
"It must be understood that the epidemiological situation is quite complicated at the moment... Currently, health services are unfortunately crowded in public and private facilities", Borba said.
In previous weeks, corruption scandals and the lack of medicines triggered demonstrations to reject the mishandling of the COVID-19 pandemic and demand Paraguay's President Mario Abdo Benitez's resignation.
As of Monday morning, the South American nation had confirmed 180,014 COVID-19 cases and 3,476 related deaths.