Government spokesman Mike Omeri told a news conference in Abuja that there was "nothing on the ground to prove any act of abduction, as reported".
A local government official in the Damboa district of Borno, a vigilante leader and an area senator had on Monday said that all the women and girls, some as young as three, were taken during a raid on Kummabza village in the last week.
Nigeria's military initially did not confirm or deny the abduction and Borno governor Kashim Shettima on Monday ordered an urgent probe, highlighting a recent reported abduction of at least 20 nomadic women from the same area.
Omeri claimed that Shettima had established "that there were no sufficient facts on the alleged abduction".
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"We hereby wish to state that based on available facts before us there was no abduction of 60 persons in Borno state," Omeri added.
Nigeria's government was heavily criticised for its slow response to the mass abduction by Boko Haram militants of more than 200 schoolgirls from the town of Chibok, also in Borno, on April 14, that triggered global outrage.
Police in Borno said that 276 girls were kidnapped and that 53 escaped in the days following the attack. On May 28, the authorities said that four more girls than previously thought had escaped, leaving 219 still held hostage.
The figures were confirmed in a report submitted to the government by a presidential fact-finding committee this week.