She says she will step down as of September to spend time with her family and out of concern for the health of her parents and husband in New Brunswick.
Lavallee, a veteran of the Canadian Forces and a member of the Mi’kmaq people, has been head of the organization since 2009.
She replaced Patrick Brazeau after he resigned to enter the Senate.
She says she's leaving the organization in good shape, financially and administratively.
She also says it's time for new leadership, especially with the Supreme Court of Canada poised to deliver a verdict in a major case which she says will bring long-sought recognition for Metis and non-status Indians.
"I feel it is the right time for new leadership to take on the challenge of pursuing the implementation of that decision," she said.
Lavallee said family needs have come to the fore.
"A person gives up a lot to serve in this kind of position and I have been happy to do it, in fact it has been a great privilege, but there comes a time to focus on family," she said.
Since 1971, the congress has promoted the rights and interests of off-reserve natives, both status and non-status, as well as the Metis and the southern Inuit of Labrador.
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