The assailants also set fire to a vehicle and destroyed property.
There has been tension in Ebonyi since a branch of the outlawed Indigenous People of Biafra (IPOB), led by Simon Ekpa, issued a stay-at-home order.
Friday, IPOB planned a "stay-at-home" from December 9 to 14 in the South-East.
Friday Nnanna, head of the Ebubeagu security unit, told reporters in Abakaliki that IPOB did not attack the Nwakpu market.
Mr. Nnanna indicated that the assailants were likely thieves.
It transpired that some boys invaded the market to plunder merchants. They are not IPOB members. "However, they entered the market with pistols made locally," added the Ebubeagu captain. Currently, an investigation is underway. We are on course to obtain them. We are focusing our spotlight on them in order to apprehend them.
The Ebonyi police command's spokesman, Chris Anyanwu, also confirmed the attack.
