Canadian Prime Minister Justin Trudeau on Tuesday said he was surprised his veterans affairs minister quit amid allegations she had been pressured to go easy on a major firm when she was justice minister.

Trudeau told reporters that Jody Wilson-Raybould had not raised any concerns with him about how Ottawa was handling the case of construction company SNC-Lavalin Group Inc, which is seeking to avoid a corruption trial because the executives accused of wrongdoing have left the company and it has overhauled ethics and compliance systems.

"Frankly, I am both surprised and disappointed by her decision to step down," Trudeau told reporters in Winnipeg, insisting the Liberal government had done nothing improper.

Trudeau would hold a press conference later Tuesday, in which he is expected to answer questions on Wilson-Raybould's resignation, according to a statement from the Prime Minister Office.

The statement said Defense Minister Harjit Sajjan immediately assumes responsibilities as acting minister of veterans affairs.

The resignation is the second blow for Trudeau in two days over the affair. Wilson-Raybould's resignation is expected to prompt another cabinet shuffle.

"With a heavy heart I have submitted my letter of resignation to the Prime Minister as a member of Cabinet," Wilson-Raybould said in her Twitter post.

Her resignation came amid an ongoing parliamentary investigation into whether Trudeau or anyone in his office tried to have Wilson-Raybould abandon the prosecution of a case against SNC-Lavalin when she was justice minister and attorney general.

Independent ethics commissioner Mario Dion said on Monday he was probing possible wrongdoing by top officials, which was welcomed by Trudeau.

Wilson-Raybould, 47, appointed justice minister when Trudeau came to power in November 2015, is one of the most prominent aboriginal politicians in federal politics.

(With input from Xinhua News Agency and Reuters)

(Cover: Canadian Prime Minister Justin Trudeau speaks with Minister of Justice Jody Wilson-Raybould during a swearing-in ceremony at Rideau Hall, November 4, 2015, Ottawa. /VCG Photo)