Those statements include the salaries and expenses of the band chiefs and councillors.
Of 582 First Nations, 48 have not complied, according to the office of the minister of aboriginal affairs.
The six bands being taken to court are those that have explicitly indicated their intention not to adhere to the First Nations Financial Transparency Act. They are the Thunderchild, Ochapowace and Onion Lake First Nations in Saskatchewan and the Sawridge, Athabasca Chipewyan and Cold Lake First Nations in Alberta.
"First Nations, like all Canadians, deserve transparency and accountability from their elected leaders. That is why we passed the FNFTA which empowers First Nation members to ensure band revenues are used for the benefit of the entire community," said Aboriginal Affairs Minister Bernard Valcourt in a statement emailed to CBC News.
Valcourt said that the government will continue to withhold funding for non-essential programs for all non-compliant First Nations.
According to a letter previously obtained by CBC News, the government outlined to First Nations the various measures it can take against them if they don't follow the law, including the halting of new funding or the cessation of funding agreements entirely.
Onion Lake Cree Nation in Alberta and Saskatchewan, one of the six bands targeted, is itself taking the federal government to court over the law. In a news conference last month, Onion Lake Chief Wallace Fox said the band's legal action was in response to the government's "ultimatum" and "threatening letters."
Valcourt is directing the Department of Aboriginal Affairs to bring its own applications to Federal Court to get an order requiring the six bands to publish their financial statements "for the benefit of their members."
This latest move comes on the eve of the Assembly of First Nations Special Chiefs' Assembly in Winnipeg, where First Nations will hold elections for a new national chief.
The AFN has previously slammed the government's handling of the transparency act as "heavy-handed."
"That they are now threatening First Nations with further punishment if they do not comply with their own flawed legislation is consistent with this colonial approach," said AFN Alberta Regional Chief Cameron Alexis in a statement.
"Recent findings that the government has been quietly shuffling and reallocating money from infrastructure to other programs indicate the government should stop lecturing First Nations and abide by their own principles of accountability and transparency," he said.