Trudeau's decision follows a complaint by the Grace Foundation of Saint John, N.B. last week, saying they lost thousands of dollars after they paid Trudeau $20,000 to speak at an event nine months ago.
"I have decided to reach out to all the organizations that hired me as a professional speaker while I was a Member of Parliament to engage with them to find a satisfactory solution," Trudeau said in a written statement on Sunday.
Grace Foundation board member Susan Buck, in a letter to Trudeau circulated by the Prime Minister's Office, asked the Liberal Leader to repay the speaking fee saying the event was "a huge disappointment and financial loss."
"I am open to exploring all options with them to ensure that they are satisfied with the outcome," the Liberal Party leader said.
Reached by phone on Sunday by CBC News, Buck said she had not personally heard from Trudeau yet and referred all further requests for comments to the board's chairperson, Ian Webster.
In a telephone interview with CBC News on Sunday, Webster said there was "no animosity" between the Grace Foundation and Trudeau.
Webster said board members would be meeting this week to come up with "a proper response" to Trudeau's offer.
Meanwhile, the Conservative MP for Fundy Royal, N.B. said he doubts the sincerity of Trudeau's offer to the Grace Foundation.
In a written statement, Rob Moore said "only when embarrassed in the media" did Trudeau agree to repay the charity. "Trudeau did not go far enough, he did not categorically commit to repay the Grace Foundation and the many other charities across the country who deemed his services a 'big disappointment.'"
NDP ethics critic Charlie Angus thinks it was inappropriate for Trudeau to charge charities for speaking engagements.
In a telephone interview with CBC News on Sunday, Angus also questioned whether Trudeau's offer to the Grace Foundation was motivated by political expediency.
"The question is whether or not he's making this offer because it's political damage control or because he's come to the realization that it was completely unethical for a Member of Parliament to be charging fees, especially outrageous fees, to charities and schools," Angus said.
Saskatchewan Premier Brad Wall, who last Friday had called on Trudeau to repay the speaking fee, tweeted on Sunday "this is very much the right thing to do @JustinTrudeau. Thank you."
Wall had also questioned whether Trudeau used the money he received from speaking fees to help finance his leadership campaign.
The controversy over whether MP's ought to charge speaking fees began last February, during the Liberal leadership campaign, when Trudeau opened up his personal finances to the Ottawa Citizen newspaper producing among other details a list of speaking fees he received for hosting events before he announced a run for the party's top job.
Trudeau said the federal ethics watchdog cleared his speaking engagements after becoming an MP.