Charles has been criticized by ministry officials over an alleged failure to meet the expected revenue targets by the Customs.
The cabinet paper for her removal also approved the appointment of a retired Navy officer in her place.
However, Samaraweera has now decided to withdraw the decisions in view of pressure from the president’s side, according to the sources.
At a meeting with the minister at his official residence on February 02, Charles agreed to return to her position today.
Samaraweera assured her that she would not be unfairly treated and that she would be entrusted with special responsibilities.
Charles has been urged by the opposition and anti-government trade unions not to leave the position.
Reports say she has asked for an additional secretary position at the office of either the president or the prime minister.