The raid took place before dawn yesterday in the village of Chakamari in a region known as the Extreme North, which borders Boko Haram strongholds in neighbouring Nigeria.
Cameroon, which is part of a regional force fighting Boko Haram, has been hit by a series of deadly Islamist attacks in recent months.
The attack came as Guinea offered help in the regional fight against Boko Haram whose bloody insurgency in Nigeria has increasingly spread to neighbouring states.
The vigilante, who spoke on condition of anonymity, said the attackers torched many homes before making off with the hostages.
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A police source confirmed the death toll and the number of people abducted.
A soldier at the scene confirmed finding six bodies, describing them as vigilantes.
"The villagers told us that more than 50 people had been kidnapped by Boko Haram terrorists," he told AFP.
The refugees had sought shelter in Cameroon from Boko Haram, but were rounded up and sent home as Yaounde stepped up security measures to prevent Boko Haram suicide attacks.
Last week, local sources in Cameroon said Yaounde had deported more than 2,000 Nigerians living illegally in the north of the country.
But Nigerian officials put the number far higher, saying that around 12,000 people had already been expelled, with the number expected to rise to 17,000.
The deportations came after three deadly attacks in Cameroon's far north last month which left at least 44 people dead.
"We are ready to provide any assistance asked of us... In the fight against Boko Haram," Conde said on a visit to Niger's capital Niamey.
A beefed-up task force has been set up to replace the current regional force and is due to go into action soon, according to Nigerian official.
Boko Haram's bloody insurgency has left more than 15,000 people dead since 2009 and has increasingly spread across the country's borders, with Chad and Cameroon suffering deadly suicide bombings in recent months.