The charity paid Trudeau $20,000 to speak at a fundraiser for the nursing home last summer, but ended up losing money and subsequently asked the federal Liberal leader for a refund.
The federal Conservatives have been accusing Trudeau of caring more about making money than serving the public.
Conservative MP for Fundy-Royal Rob Moore has said the charity asked him to pressure Trudeau to return his fee after a letter to Trudeau did not work.
Grace Foundation board member Susan Buck wrote to Trudeau asking for $20,000 because the event was a "huge disappointment and financial loss."
But in a statement issued late on Thursday, Webster said the board did not authorize anyone to approach Moore or any political person on the speaking fee dispute.
The statement said the board made the decision to drop the matter "after receiving no response" from Speaker's Spotlight, the agency that represented Trudeau as a speaker.
But in an email to CBC News Thursday, Speaker's Spotlight president Martin Perelmuter said his company did respond to Buck's letter.
'Confused' by request
"I have e-mail correspondence dated April 9th, between one of my staff and Sue Buck (on behalf of the Grace Foundation), confirming that we received the letter," Perelmuter said.
"My staff member indicated that we were confused by the request for a refund, since we had followed up after the event, nine months prior to receiving the letter, and were told that the Grace Foundation was pleased with the outcome, and Justin’s presentation."
A well-placed source told CBC News the board did not know about Speaker Spotlight's response and, even if it had, it would not have changed the board's decision to drop the matter in any case.
Board member Judith Baxter gave the Buck letter to Moore. Baxter, who posted a photo of herself on Facebook visiting the Prime Minister's Office in February, received a Jubilee medal from Moore, and her husband, Glen, is on the executive of Moore's riding association.
Trudeau, who was an MP at the time of the fundraiser, has offered to compensate charities that paid him to speak at events. He stopped accepting paid speaking engagements last year when he decided to run for the leadership of the Liberal Party.
The statement from Webster said the board is "deeply distressed about many statements made from various persons."
"We believe our correspondence this week with Mr. Trudeau will be helpful in clarifying the misunderstanding between Mr. Trudeau and ourselves."