Commissioner for Health, Professor Akin Abayomi, announced the new deaths on Tuesday.
One of them was a 45 year-old man, who returned from India in January.
The second was a 36 year old woman who had a severe underlying health problems.
Abayomi tweeted that the woman had no history of travel or contact with any confirmed case of coronavirus.
He urged residents to remain vigilant and report any concern about COVID-19 infection in their various communities.
Lagos is the worst hit state by the virus with 379 infections.
It has till date 260 active cases remaining.
According to Abayomi, 98 patients have been discharged and 16 have died.
Significantly, Lagos recorded zero new case on Monday.
☑️No new case of #COVID19 was confirmed in Lagos on 20th April, 2020.
☑️However, #COVID19 related deaths were recorded in Lagos. One of the deceased was a 45 years old Nigerian🇳🇬; male who returned from India in January, 2020.@jidesanwoolu @NCDCgov pic.twitter.com/qGL9aalxDw
— Prof. Akin Abayomi (@ProfAkinAbayomi) April 21, 2020