Ellen Johnson-Sirleaf, Africa's first elected female head of state, relieved employees appointed by the outgoing caretaker government of their posts.
She told employees during a surprise visit to the ministry late on Wednesday: "Those who are part of financial malpractices and scandals must give way for those who are prepared to do the will of the Liberian people".
Living up to her reputation as an "Iron Lady", Johnson-Sirleaf said her victory in November's presidential election run-off gave her a mandate to clean up Liberia's finances.
She named Antoinette Sayeh, a former World Bank official, as finance minister, with a brief to root out graft and build bridges with international donors, who have made further aid contingent on weeding out corruption.
With a debt of over $3 billion, the West African nation is reliant on aid from the United Nations, the World Bank, the United States and Europe.
Endemic corruption was a key cause of Liberia's civil war, which killed 250,000 people and devastated Africa's oldest republic, founded by freed American slaves in 1847.
Johnson-Sirleaf, a 67-year-old Harvard-trained economist, pledged at her inauguration last month to make the war on corruption a priority.
Facing a Herculean task of rebuilding a nation shattered by 14 years of civil war, the new government took its first significant step towards tackling corruption on Tuesday when it banned members of the previous transitional administration from leaving Liberia until they had undergone a financial audit.
Widespread theft during a two-year interim regime scuppered Liberia's efforts to rebuild after a peace deal was signed in 2003.
"Those who are part of financial malpractices and scandals must give way for those who are prepared to do the will of the Liberian people"
Ellen Johnson-Sirleaf, the president of Liberia
The capital Monrovia is still without state-supplied electricity or piped water and many buildings remain derelict.
Johnson-Sirleaf said all political appointees and members of the transitional government would be removed from their posts.
"No one should consider themselves as civil servants," she said.
Johnson-Sirleaf pledged to honour a donor-backed programme under which foreign experts will oversee state spending: the Governance and Economic Management Programme (GEMAP).