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Speaker Lockwood Smith confirmed to NZPA that his office received the letter of resignation this afternoon.
Mr Harawira said his resignation would be effective from May 20 and the date of the by-election was now in Dr Smith's hands.
"I am comfortable with my decision to put the future of the Tai Tokerau in the hands of the people, and I welcome the challenge of others seeking the mandate of the north," he said.
The Maori Party and Labour this week confirmed they would be standing candidates against Mr Harawira, but National has indicated it would stay out of the race.
Mr Harawira said today he hoped the campaign would be fought on the records of the candidates and the policies of the parties.
"The people of Tai Tokerau deserve the opportunity of a clear campaign, devoid of all the nasty innuendo of the past few weeks."
Dr Smith told NZPA the matter would now go to the Electoral Commission.
"Obviously he resigns his seat, he will no longer be paid as a Member of Parliament, there are ramifications for how long his electorate office can continue to operate," he said.
The by-election would cost about $500,000 to run and would likely be held close to the general election.
The contest has already turned ugly, with Mr Harawira and the Maori Party trading accusations.
Mr Harawira says the Maori Party's decision to stand against him breached an agreement he entered into with the party after he quit in February over the Maori Party's relationship with the Government.
But the Maori Party says Mr Harawira breached the agreement first by saying he would quit Parliament to force the by-election.
Maori Party co-leader Tariana Turia yesterday revealed two party members had been sent threatening emails after a hui at Te Tii Marae in Waitangi on Sunday.
During the hui attendees endured a sustained, abusive rant from Titewhai Harawira, Mr Harawira's mother, according to Maori Party leaders.