Prime Minister Stephen Harper and then-national chief for the Assembly of First Nations Shawn Atleo signed an agreement on amendments to the controversial aboriginal education bill after the initial draft was rejected, according to a court document.

The document was filed by the government in federal court Wednesday as part of its defence to prevent a judicial review of the First Nations Education Act.

The Assembly of First Nations of Quebec and Labrador are fighting the bill. First Nations leaders didn't like the initial draft because it didn't give them enough control over education and didn't guarantee new funding.

The four-page document signed by Harper, Atleo and Aboriginal Affairs Minister Bernard Valcourt says "substantive amendments" were made to the draft of the bill, which was proposed by the Conservatives in October 2013.

The bill was amended to "require that elders, parents and students be meaningfully involved in the decision making processes in their community's education."

The document brings into question the legitimacy of the Act, the agreement and a February press conference where Harper and Atleo stood side-by-side at the Blood Tribe reserve in Alberta to announce $1.9 billion in federal funding.

"The legislation will end Ottawa's unilateral authority over First Nations education while requiring First Nations communities and parents to assume responsibility and accountability for the education their children receive," said Harper at the time.

Harper and Atleo announced they had reached a "historic agreement" knowing they had a signed document outlining the new bill. According to APTN, Atleo's own executive didn't know about the deal and the agreement was only with Atleo, not the AFN.

Atleo resigned as national chief in May saying he didn't want to be a "lightning rod" in the debate over the education bill. He was heavily criticized for supporting the bill. Chiefs from several provinces voted to reject the Act arguing Ottawa failed to consult them. The Act is now in limbo, along with the $1.9 billion in new funding.