The assailants tied up the agricultural workers and slit their throats in the village of Koshobe, the militia said.
President Muhammadu Buhari condemned the attack, saying: “The entire country has been wounded by these senseless killings.”
“We have recovered 43 dead bodies, all of them slaughtered, along with six others with serious injuries,” said militia leader Babakura Kolo, who helped the survivors.
“It is no doubt the handiwork of Boko Haram who operate in the area and frequently attack farmers.”
The victims were labourers from Sokoto state, roughly 1,000 kilometres (600 miles) away, who had travelled to Borno to find work, said another militiaman Ibrahim Liman who gave the same toll.
“There were 60 farmers who were contracted to harvest paddy in the rice fields. Forty-three were slaughtered, with six injured,” Liman said.
Eight others were missing, presumed to have been kidnapped by the jihadists, he said.
The bodies were taken to Zabarmari village, two kilometres away, where they would be kept ahead of burial on Sunday, said resident Mala Bunu who took part in the search and rescue operation.
Last month Boko Haram militants slaughtered 22 farmers working on their irrigation fields near Maiduguri in two separate incidents.
Boko Haram and ISWAP, its IS-linked rival, have increasingly targeted loggers, herders and fishermen in their violent campaign, accusing them of spying and passing information to the military and the local militia fighting them.
At least 36,000 people have been killed in the jihadist conflict, which has displaced around two million since 2009.
The violence has also spread into neighbouring Niger, Chad and Cameroon, prompting a regional military coalition to fight the militants.
The attack took place as voters went to the polls in local elections in Borno State.
The elections had been repeatedly postponed because of an increase in attacks by Boko Haram and ISWAP.