While neighbouring Liberia has defeated Ebola, Sierra Leone and Guinea have continued to battle new cases, particularly along the border where those two countries meet.
Sierra Leone had 15 news cases in the week ending June 7, according to the World Health Organisation, the highest weekly total since late March.
On Friday, President Ernest Bai Koroma said people would be barred from entering or leaving the affected parts of Kambia and Port Loko districts in northern Sierra Leone.
Eleven of the country's 14 districts have gone more than 42 days without an Ebola case - the benchmark for declaring an epidemic over. Another has gone nearly two weeks without a new case.
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"I do not believe it is fair for most districts to have gone for more than 42 days without recording a single case of Ebola, and these two districts are holding us to ransom," Koroma said.
"We are going into those districts with a sledgehammer," retired Maj. Alfred Palo Conteh, who heads Sierra Leone's National Ebola Response Center, said in a radio interview.
Ebola has claimed more than 11,000 lives in West Africa since December 2013, including more than 3,900 in Sierra Leone.
Sierra Leone's parliament this week extended the country's state of public health emergency for another three months. The country has previously used "lockdowns" to keep residents in their homes so that authorities can attempt to identify the sick who were not being treated at Ebola centers.