The reason for Jayawardena's removal is not known.
Her removal came amid easing of the nearly two-month coronavirus lockdown in the island nation.
Major General Sanjeewa Munasinghe has replaced Jayawardena, who has been transferred to the Ministry of Internal Trade and Consumer Affairs in the same capacity, officials said.
Before assuming his current position, Munasinghe was serving as the Director General of the Army Medical Services. He is also a former Colonel Commandant of the Army Medical Corp.
Meanwhile, President Rajapaksa ordered easing of the lockdown, which was in force since March 20 to combat the spread of the coronavirus.
The deadly virus has claimed nine lives and infected 863 people in the nation.
A 24-hour curfew was lifted on the island, except for Colombo district.
The state and private sector offices were asked to follow strict health guidelines under quarantine ordinance.
Public transport operation was less than normal on Monday. CORR SCYSCY