Troops have taken control of the remote region bordering Bangladesh since October 9 when armed men raided police posts, killing nine officers.
At least 34,000 Rohingya Muslims have since fled to Bangladesh, taking with them allegations of mass-killings, rape and torture at the hands of Myanmar security forces.
The Myanmar government has vigorously denied the accusations, setting off the latest war of words over a stateless minority whose status is one of the country's most incendiary issues.
Police did not give a motive for the killing of the 41-year-old man, whose body was found floating in a river, but said he spoke to Burmese journalists on Wednesday in Ngakhura village.
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Shu Nar Myar, seen speaking to reporters during the Rohingya crisis in the Rakhine state AFP
"On Thursday his family said he had disappeared after giving interviews to journalists," Police Colonel Thet Naing in Maungdaw town told AFP.
"This afternoon (Friday) I got the report his headless body was found... we have confirmed from villagers that it is him," he said, adding police went to the scene of the grisly find.
Troops have killed more than 80 people in Rakhine since the start of crackdown, according to official figures.
Conflict analysts the International Crisis Group (ICG) say militants behind the border post attacks have also killed several Rohingya 'informers' perceived to be working with the Myanmar authorities.
In a statement on Friday, the President's Office confirmed that a man -- whom they identified as Shu Nar Myar -- had been killed, adding that he had denied stories of military abuse when speaking to the reporters.
"Shu Nar Myar is the one who revealed that there was no case of arson by the military and police forces, no rape and no unjust arrests," the statement said.
Two Burmese reporters, who did not want to be named, told AFP that they interviewed the man on Wednesday at his village and had been contacted by police to say he was missing.
The rare media tour of the area -- open only to Burmese journalists -- was organised by the government amid mounting pressure on de facto civilian leader Aung San Suu Kyi to allow access to the conflict zone.
Her government has responded to growing international alarm over the crisis with a dogged information campaign aimed at batting back reports of military abuse.
Northern Rakhine has been under lockdown for more than two months since the hundreds of armed militants launched surprise attacks on border posts.
ICG says the attackers are from a Saudi-backed group called Harakah al-Yaqin which emerged after a wave of sectarian violence cut through Rakhine in 2012.
The Rohingya have languished under years of dire poverty and discrimination from a government that denies them citizenship.
The UN and other rights groups have repeatedly called on Myanmar to grant them full rights, describing the Rohingya as one of the world's most persecuted minorities.