President Denis Sassou Nguesso's government "decided to withdraw" the troops deployed in the MINUSCA mission after the commander complained of misconduct, a UN statement said.
"The review of the deployment of uniformed military personnel from the Republic of Congo found that the nature and extent of existing allegations of sexual exploitation and abuse, in their totality, point to systemic problems in command and control," it said.
"These problems have also been compounded by issues related to the preparedness, overall discipline, maintenance of contingent-owned equipment, and logistical capacity of these troops."
The 12,000-strong MINUSCA force has been plagued by a wave of sexual abuse allegations since the mission to help restore stability to the country began in 2014.
Lieutenant-General Balla Keita of Senegal told UN headquarters in a leaked memo he had sent six letters of blame to the battalion commander already this year over alleged sexual abuse, fuel trafficking, and lack of discipline.
A quick overview of CAR crisis
The 629 peacekeepers deployed in Berberati, the country's third-largest city, are Brazzaville's only contribution to UN peacekeeping.
Despite the departure of the troops, a smaller contingent of 140 police from Congo will remain in the mission in the Central African Republic, the UN said.
Last year, 120 troops from the same contingent were sent back following allegations of sexual abuse and exploitation involving at least seven victims, six of whom were children.
"The battalion is notorious for SEA [sexual exploitation and abuse] misconducts, fuel trafficking, and poor discipline," Keita wrote in the memo sent last month.
"The situation has deteriorated to the point that the battalion is no longer trustable because of poor leadership, lack of discipline, and operational deficiencies," he added.
Former UN chief Ban Ki-moon in 2015 took the rare step of firing the then-head of the peacekeeping force over his handling of dozens of misconduct cases, including the rape of minors.
With sex abuse cases continuing to surface, Ban's successor Antonio Guterres has vowed to toughen the response to the damaging allegations as he faces pressure from the United States to cut funding for peacekeeping.
UN critics in the United States - many of whom are in the US Congress - point to the mounting cases of misconduct by UN peacekeepers to support their campaign to cut funding to UN missions.
The memo and UN assessment of the Congolese troops were released by the Code Blue Campaign of non-governmental organisations seeking to expose cases of sexual abuse and exploitation by UN peacekeepers.
Code Blue said in a statement it was relieved by the decision that "will ensure that vulnerable women and children in Berberati will be safe from further predation by that particular battalion".
But the group asked why the United Nations waited until documents were leaked to take a decision and said the world body must now ensure that soldiers facing credible allegations are prosecuted by Brazzaville authorities.
Under UN rules, it is up to the country contributing troops to a peacekeeping mission to investigate and prosecute criminal cases.