The doctors' walkout was triggered in part because they said they lost between 20% to 40% of their take-home pay in May after the government ended their monthly COVID-19 risk allowance and a tax break they had received with the onset of the pandemic.
They are also demanding fuel allowances of 45 liters per week, which they said has been promised but not delivered for years.
The government said it has met the doctors' demands and that salaries would be increased in September. Fuel vouchers will also be given out weekly, said health minister Austin Demby.
"It is very, very difficult to understand why a strike is needed," Demby said.
But the backlog of extra pay due since May has not been addressed, and doctors don't trust the fuel allowance system, said Edries Tejan, president of the Medical and Dental Association.
"The doctors are not convinced that particular system they are proposing is going to work," he said.
Doctors also staged strikes in 2018 and 2020 in the West Africa country, protesting low pay, poor working conditions and unpaid bonuses. Sierra Leone has some of the worst health outcomes in the world.