The government has launched the "Zero Ebola" campaign in which almost all Sierra Leoneans are supposed to stay indoors on and between March 27-29 and from 6 a.m. to 6 p.m. on three consecutive Saturdays -- April 4, 11 and 18.
But it has now said Christians will still be able to gather for worship, sparking debate on the issue across the country, according to Christian Aid.
"The whole issue of congregational prayers is a tricky one because Sierra Leone is a hugely religious country where everyone has one religion, said Jeanne Kamara, Sierra Leone, country manager Christian Aid.
"The government actually made an exception for Palm Sunday because Christianity is quite big here and of course Palm Sunday is an important part of the Christian calendar."
"Apparently the government fell to that, they had to kind of adjust the lockdown to take on board the needs of Christians on Palm Sunday," she added.
According to a 2009 estimate 71.3% of the population is Muslim with just 26.8% being Christian.
It comes as health experts say the Ebola outbreak is far from coming to an end.
The charity Medecins Sans Frontieres claims governments in the region did not share enough information when it first started.
It has also criticised the initial slow response of the World Health Organisation.
The virus has killed more than 10,000 people in the last 12 months.
Jeanne Kamara, Sierra Leone, country manager Christain Aid:
