The Nigerian Centre for Disease Control (NCDC) says at least 812 health workers have tested positive for coronavirus.
Chief Executive Chikwe Ihekweazu said on Tuesday that 29 of the infected health workers are staff at the agency.
Nigeria has confirmed 10,819 cases and 314 deaths so far.
In April, the Nigerian Medical Association attributed the infection of front-line health workers to lack of adequate protection.
But Mr Ihekweazu said the centre had distributed 40,000 pieces of Personal Protective Equipment (PPE) to the workers.
Unions of health workers in some states have threatened strike action over lack of adequate protective gear.
Meanwhile, the government has reversed its earlier directive that prohibited private hospitals from treating Covid-19 patients.
It has asked private hospitals to register with their respective state governments and ensure proper training of staff.