Rajkhowa "shall cease to hold the office of the Governor of Arunachal Pradesh", said a Rashtrapati Bhavan communique.
Meghalaya Governor V Shanmuganathan has been asked by the President to discharge the functions in addition to his own duties, until regular arrangements are made, it said.
Appointed Governor of Arunachal Pradesh on May 12 last year, Rajkhowa is the first NDA gubernatorial appointed to be sacked with the government informing that President that it has "lost trust" in him.
The Home Minister's meeting with the President came after Rajkhowa refused to step down despite a nudge by the Centre to put in his papers after the Supreme Court passed serious strictures against him over the dismissal of the Congress government last year.
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A defiant Rajkhowa had said he would not step down but was ready to be sacked.
Rajkhowa had said he was asked to resign "on health grounds" weeks after the Supreme Court had restored the Congress government in Arunachal Pradesh and censured him.
Rajkhowa had also written to the President explaining his position and the letter was forwarded to the Home Ministry by Mukherjee.
However, when the Home Ministry submitted a detailed report on the Governor to the President, he finally sacked Rajkhowa today.
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