Aboriginal Affairs Minister John Duncan has resigned from cabinet over an inappropriate letter he wrote to the Tax Court two years ago, a mistake seen as inexcusable that gives the Conservative government an opportunity to shed one of its weaker performers.

Mr. Duncan announced late on Friday that he was quitting his post because of a 2011 letter he wrote to the Tax Court of Canada on behalf of a constituent.

"While the letter was written with honourable intentions, I realize that it was not appropriate for me, as a Minister of the Crown, to write to the Tax Court," he said in a statement. "I take full responsibility for my actions and the consequences they have brought."

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Government sources insist Mr. Duncan's departure was not connected to dissatisfaction with his performance. Rather, an internal review was triggered in ministers' offices because of recent rulings by Ethics Commissioner Mary Dawson. Last month, she declared that Finance Minister Jim Flaherty and two parliamentary secretaries – Eve Adams and Colin Carrie – acted improperly in writing letters to the CRTC in support of constituents competing for a Toronto radio licence.

Prime Minister Stephen Harper did not announce any disciplinary action in those cases. A source said a letter to a judge is seen as a more serious breach than letters to the CRTC, and pointed to precedents under previous governments.

However, Mr. Duncan appeared to be sidelined as aboriginal issues heated up early this year through Idle No More protests and the high-profile hunger strike by Attawapiskat Chief Theresa Spence.

The Prime Ministers' Office led and hosted a meeting between the government and native leaders last month. Mr. Harper promised further high-level meetings with the Assembly of First Nations on issues like treaty rights.

Those meetings continue behind the scenes, but the process is said to be driven more by Mr. Harper's senior staff, such as policy director Rachel Curran, than by the aboriginal affairs minister.

Derek Nepinak, the Grand Chief of the Assembly of Manitoba Chiefs, said Mr. Duncan's resignation was not a surprise.

"I think it's a very stressful portfolio to hold in and of its own, but particularly when he's being asked to push forward a legislative reform package that nobody really agrees with," he said.

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Mr. Duncan knew his files well as a former aboriginal affairs critic and an MP for Vancouver Island North, which has a large aboriginal population. However, he was widely seen as a poor communicator, and native leaders did not feel he held much sway in cabinet, unlike predecessors Jim Prentice and Chuck Strahl.

Mr. Duncan has a heart condition, and there was some suggestion that his weak performance was due to health issues. However, Mr. Harper is said to have great respect for Mr. Duncan, and he holds one of only two Tory seats on Vancouver Island, a vital and difficult battleground for Conservatives. Sources say his health has improved of late.

Canadian Heritage Minister James Moore will be acting minister of aboriginal affairs and northern development until a replacement is named.

New ministers taking on the aboriginal affairs file have a very steep learning curve, given its many historical and legal complexities and the importance native leaders place on developing trust. Few ministers relish it, and it brings little opportunity to be transformative.

The Prime Minister has signalled to fellow Tories that he will shuffle his cabinet in mid-2013 and prorogue Parliament to usher in a new Throne Speech outlining what will clearly be a pre-election agenda. Mr. Harper wants to promote strong performers, drop weaker ones and build a team for the next campaign.

Greg Rickford, parliamentary secretary to the minister, is seen as a capable communicator on aboriginal issues. Mr. Rickford, a bilingual lawyer who represents Kenora, made improving economic conditions for first nations a key campaign plank in the 2008 election. He was on a flight on Friday and not available for comment, a spokesman said.

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Jean Crowder, the NDP's critic for aboriginal affairs, said she considers the letter Mr. Duncan wrote on behalf of a constituent to be a serious error."I was surprised that an experienced member of Parliament, an experienced cabinet minister, would make a mistake like that," she said. "I was shocked."She said shewants to see a permanent aboriginal affairs minister as soon as possible.

Resignations from the Harper cabinet are relatively rare. In the seven years Mr. Harper has been in office, seven ministers, including Mr. Duncan, have resigned. Michael Chong resigned in 2006 over a disagreement with Mr. Harper's decision to recognize the Québécois as a nation; Maxime Bernier resigned in 2008 after a scandal involving secret documents; Helena Guergis was forced to resign over allegations of wrongdoing in 2010; Jim Prentice resigned in 2010 to become a senior executive at CIBC; Greg Thompson resigned in 2010 after deciding not to run in the next election; Bev Oda was dropped from cabinet in 2012 after resigning her seat. Mr. Bernier is back in cabinet as minister of state for small business and tourism.