The Ugandan player is part of Uganda's national team squad, which confronted Malawi in Africa Cup of Nations qualifiers.
A response from a laboratory in Malawi confirmed Lwanga and two other Uganda national team players have contracted coronavirus.
The midfielder could be missing after COVID-19 tests showed he was among three Ugandan players infected with the disease, with goalkeeper Denis Onyango and midfielder Farouk Miya.
The results of the trio, including Lwanga, was issued shortly before the African Cup of Nations' qualifiers' match between hosts Malawi and Uganda scheduled to be played in Lilongwe.
However, the Uganda Football Federation (FUFA) expressed its dismay and disagreement with the response to the tests, claiming that Lwanga was not infected with COVID-19.
The FUFA revealed: "We are closely monitoring the mistakes made by our team of doctors on Thadeo Lwanga's COVID-19 tests.''
''Two tests have produced two different responses. We have written to CAF on this matter," the FUFA statement said.
According to Malawi's immigration system, a person diagnosed with COVID-19 infection should be quarantined for seven days and then tested again.
As a result, Lwanga is set to miss the Simba SC v AS Vita Club match, which will take place at Benjamin Mkapa Stadium.