The exercise kicked off on Thursday morning on some roads and entry points.
Rwandan health authorities say this “will provide factual information about the Covid-19 status in the capital”.
From March, Rwanda has conducted more than 140,000 tests. More than 1,000 have recorded positive results.
Officials in Kigali told the BBC that they will be focusing on morning hours as people go to work and in the evenings as they return home.
Some are however complaining that they are being forced to consent to the testing.
A motorcyclist told the BBC he was forced by police to cooperate, while another said he was “happy to easily get tested on street” and carry on his activities.
Last week, the Rwandan authorities re-introduced a lockdown in parts of Kigali as dozens of cases were confirmed.