His detention on Thursday evening in eastern DR Congo came a day after the UN chief said he was “deeply concerned” about allegations of such mistreatment.
Ban Ki-moon’s spokesman said the UN mission was reviewing its support of those units suspected of involvement.
The army and M23 rebels began fighting near the key city of Goma on Sunday.
The BBC’s Maud Jullien in Goma says the frontline was just 7km (about four miles) away on the hills north of the city.
There have not been any clashes in the last two days and the army says they have pushed the rebels back by about 6km, she reports.
In November, the M23 rebels briefly captured Goma, withdrawing in exchange for a series of demands, including negotiations with the government.
Arrest anger
The UN mission in DR Congo had heard allegations of “serious mistreatment” by national army soldiers, which it had raised at the highest level within the military, a statement from Mr Ban’s office said on Wednesday.
“The secretary-general is deeply concerned about reports of alleged mistreatment of M23 detainees and desecration of corpses of M23 combatants by the Congolese armed forces,” it said.
DR Congo’s Information Minister Lambert Mende confirmed that there had been an arrest and named the officer as Lt Solomo Bangala, who had been fighting on the frontline in the 391st Battalion.
“He was transferred into the hands of military judicial officials for the desecration of enemy corpses,” Mr Mende told the BBC.
Our reporter says some Goma residents have been angered by the arrest, seeing it as a pretext to prevent the army defeating the rebels and make the government return to the negotiating table.
A small group of people protested on the streets of Goma to voice their unhappiness about the UN’s statement and the fact that a new UN brigade which is being deployed to take on the rebels has not intervened in the current fighting.
It followed a larger demonstration on Thursday when some UN convoys were stoned, our reporter says.
The BBC spoke to soldiers who confessed to raping women
Human rights groups have catalogued abuses by all sides, including the army, during two decades of conflict in eastern DR Congo but arrests for alleged cases of such behaviour are rare.
In April, 12 senior officers were suspended over the mass rape of civilians, also following pressure from the UN.
The UN has more than 20,000 soldiers on the ground in DR Congo and the new 3,000-strong intervention brigade has a mission to neutralise and disarm eastern DR Congo’s many armed groups.
The M23 rebels, who are mainly from the Tutsi ethnic group, mutinied and deserted from the Congolese army in April 2012, forcing an estimated 800,000 people from their homes in the ensuing unrest in the mineral-rich region.
Peace talks taking place in Uganda this year to resolve their grievances have stalled.