'Tensions have arisen at Rideau Hall over the past few months and for that, I am sorry'.
Payette offered her resignation on Thursday, after an independent review found the former astronaut presided over a toxic work environment at the vice-regal office.
In a detailed statement, Payette said that she took the allegations seriously - although she did not formally apologize or admit to any misconduct in the workplace.
Julie Payette says everyone has a right to a healthy and safe work environment.
Trudeau said her resignation "provides an opportunity for new leadership at Rideau Hall to address the workplace concerns raised by employees during the review".More news: Djokovic Says Demands For Australian Open Players 'Misconstrued'
She will be replaced temporarily by Richard Wagner, chief justice of the Supreme Court of Canada.
While the Governor General is a largely symbolic position, it does have some constitutional importance, particularly during a minority government such as the one Canada has now. The prime minister said he would submit recommendations for Ms Payette's replacement to the Queen "in due course".
"We have a responsibility to live up to a higher standard", Qaqqaq said.
Payette appoints as her top adviser Assunta Di Lorenzo, a close friend and corporate lawyer with no prior experience in protocol or the governor general's operations.
The allegations were first reported by CBC News.More news: Apple might be working on a VR headset
In his own release, Trudeau stated Payette has "fulfilled her duties to uphold parliamentary democracy and serve the public".
In 2008, then prime minister Stephen Harper asked governor general Michaelle Jean to prorogue Parliament to avoid a non-confidence vote he was expected to lose - a decision that was controversial at the time but in keeping with constitutional tradition.
The Privy Council Office has received the final report from a private investigative firm that was commissioned last September to shed light on these explosive allegations regarding the work climate at Rideau Hall, the daily reported Thursday.
Nelson Wiseman, a political science professor at the University of Toronto, said he was fairly certain that no governor general has resigned in the past.
"You get to shake hands with people, you get to be the nice person in the room", "I just don't understand why she would have such an exacting style and why that - of any office within the government - would have be the one that's most toxic".More news: HSBC to close another 82 branches
I have had the chance to meet, represent and celebrate the accomplishments of thousands of extraordinary Canadians from coast to coast over the past years and I will always cherish these memories.