Sweden, Britain and Germany announced "without prior consultation" that they were repatriating the 12 police officers, a move that affected the peacekeeping mission's operation and dealt a "serious blow to the morale" of the force, an internal UN memo obtained by AFP said.
The three countries withdrew the police from the mission known as Unmiss as fighting flared in Juba between government forces and fighters loyal to ex-rebel leader and now Vice President Riek Machar.
UN spokesman Farhan Haq said that the police "did not stay at their post" and that "those particular officers would be withdrawn and not replaced by personnel from the same nations".
Juba was rocked by three days of heavy fighting in early July that left at least 300 dead and set back efforts to implement a peace deal signed last year.
The 12 UN police left South Sudan during evacuation operations organized by their national governments.
"This was done without consulting the mission," said a UN official, who asked not to be named.
"UN peacekeeping has decided to disinvited these PCCs (police-contributing country) from returning their police officers to South Sudan and has conveyed this decision to the concerned countries," added the official.
A spokesperson for the British mission to the United Nations confirmed that two British police officers were evacuated from Juba on July 13th, and said a UN police advisor was informed of the decision.
"We judged their temporary removal was necessary for the officers' safety. Their well-being is our chief concern," said the spokesperson.
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The UN memo severely criticized Britain in particular as a Security Council member for the decision to pull its police officers from South Sudan at a time when the peacekeepers were confronted with the flareup of violence.
Sweden will serve as a member of the Security Council during the 2017-18 period.
"For some TCCs (troop-contributing country) who are council members and have the responsibility to ensure peace and security globally, this can be considered as a lack of respect to their engagement on peace and security," said the internal memo.
It went on to say that this raises questions about Security Council members who give instructions to "others on how to handle peace and security issues when they themselves are quick to abandon their post in challenging situations".
The withdrawal of seven police officers from Germany and two from Britain put an end to their participation in the Unmiss police force. Sweden has pulled three out of the nine police officers serving in the force.
Norway is planning to repatriate one officer on medical grounds and the United States is planning to withdraw nine out of the 15 officers in South Sudan, said the memo.
The document recalled that hundreds of UN civilian staff, UN volunteers and non-governmental organizations "remain in Juba, carrying out their duties to the extent possible under extremely challenging circumstances".
There are about 1200 police serving in Unmiss alongside military contingents. There are about 13,500 peacekeepers in all.
The police and troops serving in Unmiss are tasked primarily with protecting civilians in South Sudan, which has been torn apart by war since 2013.
In Juba, 32,000 civilians are sheltering in two UN peacekeeping compounds, and UN-protected bases across the country are offering protection to tens of thousands of South Sudanese.