Treasury Board President Jane Philpott said she must abide by my core values, her ethical responsibilities, and constitutional obligations.
Mr Trudeau has however, denied political meddling in an investigation into engineering giant SNC-Lavalin. The opposition leader last week called on the prime minister to resign.
Ms Philpott announced her decision to step down on Monday, posting her resignation letter detailing her serious concerns with evidence of efforts by politicians or officials to pressure the former Attorney General to intervene in the criminal case involving SNC-Lavalin”.
In her resignation letter, she said there can be a cost to acting on one’s principles, but there is a bigger cost to abandoning them. The former family physician has held key portfolios in Mr Trudeau’s cabinet health, indigenous services and, until this week, treasury board president – since being elected in 2015. She will remain as a member of the Liberal caucus.
This is the third high-profile resignation following accusations Mr Trudeau and some of his top aides tried to shield one of the country’s biggest firms from a corruption trial. Former attorney general and justice minister Jody Wilson-Raybould resigned suddenly from Cabinet in February.
Ms Wilson Raybould has said she and her staff faced four months of a “sustained” and “inappropriate effort” late last year to push for a possible deferred prosecution agreement for the Quebec-based engineering and construction company.
The agreement, would have enabled the firm to avoid a criminal trial and instead tends to agree to alternative terms or conditions, like penalties or enhanced compliance measures.
The company and two of its subsidiaries had faced fraud and corruption charges in relation to about $48m, ($36m; £28m) in bribes it is alleged to have offered to Libyan officials between 2001 to 2011.
On 18 February, Mr Trudeau’s top aide, Gerald Butts, announced he was resigning, denying in a statement that he or anyone on his staff had done anything wrong but saying he had to leave so as not to distract the vital work being done by the team.