In a letter dated Jan. 7, obtained by The Canadian Press, Buckingham Palace tells a supporter of Spence that the chief should deal instead with the federal cabinet.
"This is not a matter in which The Queen would intervene," says the letter.
"As a constitutional Sovereign, Her Majesty acts through her personal representative, the Governor General, on the advice of her Canadian Ministers and, therefore, it is to them that your appeal should be directed."
The letter also says the Queen understands the concerns about the welfare of Spence, who is now well into her sixth week of protest, surviving on fish broth and tea.
"Her Majesty has taken careful note of the concern you express for the welfare of Attawapiskat First Nations Chief Theresa Spence who is currently on a politically motivated hunger strike in Canada."
The response is addressed to Jonathan Francoeur, a small businessman in British Columbia who took it upon himself to write to the Queen on Dec. 15. It is signed by Miss Jennie Vine, deputy to the senior correspondence officer.
A spokesman for Spence said he believed the letter to be a fake, but he also said he did not know Francoeur. He did not respond to questions about why he believed the letter was not genuine. Francoeur said he wrote the letter on his own initiative and not in an official capacity. There is a long Facebook trail starting Dec. 15 describing the process he went through to write the letter, decide the content and post it. Francoeur received the response earlier this week and said there was absolutely no reason to believe the response was a fake.
Joanne Charette, spokeswoman for Rideau Hall, also said the letter looked genuine.
A spokesperson for Buckingham Palace said they would not comment on personal correspondence.
"I was reading a (Facebook) post and it was explaining the cause," Francoeur said in a telephone interview, when asked why he wrote to Buckingham Palace.
"It said to support the cause, it would be good for somebody to write the Queen and the prime minister."
Francoeur said he was at home nursing a broken toe and had time on his hands to compose the letters. He has not yet heard back from Prime Minister Stephen Harper, so now he has written to the Queen a second time.
"I can't communicate with the prime minister," he said. "I wanted her to know."
Spence is camped out on Victoria Island, within site of the Parliament Buildings, where she says she will continue to protest until the Governor General and the prime minister meet all chiefs on the plight of First Nations people.
She announced last week she would boycott a meeting between the Assembly of First Nations and Harper because the Governor General would not be attending.
"We have sent a letter to Buckingham Palace, requesting that Queen Elizabeth II send forth her representative, which is the Governor General of Canada," Spence said in a statement on Jan. 9.
By that day, the response from the palace to Francoeur was already in the mail. The Queen's response was circulated among chiefs and Spence supporters this week.
While the letter may remove the palace from any official role in the controversy, it does send a signal to the prime minister that he bears great responsibility for the lengthy protest by Spence, said Isadore Day, chief of the Serpent River reserve near Elliot Lake, Ont.
"The prime minister needs to have a little bit of moral reflection," Day said.
The fact the Queen wrote back at all is telling, he said.