Ambassador Macharia Kamau charged that "certain current and future members of the Security Council" had pushed for a probe with a "pre-ordained outcome" that targeted the Kenyan general as the "fall guy."
UN Secretary-General Ban Ki-moon on Tuesday sacked Lieutenant General Johnson Ondieki after the investigation showed that peacekeepers failed to protect civilians during heavy fighting in Juba in July.
"The United Nations acquiesced to undertake the investigation with skewed terms of reference meant to target one individual," said Kamau, who slammed the report as "shameful, unfair and an exercise in scapegoating."
The ambassador did not name the countries involved, but China's peacekeepers in South Sudan were criticized in the report, and Ethiopia, which has troops in the mission, is due to join the council in January.
Ondieki has been replaced as force commander by Major-General Chaoying Yang of China.
After learning that the report would recommend the dismissal of Ondieki, Kenya sought to intervene with Ban to defend the general, who had been in the post for three weeks.
"The secretary-general in his lame-duck season seems to have found the courage that has eluded him throughout his tenure by choosing to ignore Kenya's plea," said Kamau in pointed criticism of the UN chief.
Kenya responded to the UN decision by announcing that it will pull its 1,050 troops out of South Sudan and dropped plans to contribute soldiers to a planned UN regional force for Juba.
UN spokesman Stephane Dujarric defended the sacking of the force commander, saying it was based on "leadership command decisions" taken by Ondieki during the fighting in July.
"There was no pre-ordained conclusion to Mister Cammaert's work," he said. Retired Dutch general Patrick Cammaert led the investigation.
The report found that a lack of leadership in the UN mission culminated in a "chaotic and ineffective response" during heavy fighting in the capital from July 8 to 11.
Peacekeepers abandoned their posts and failed to respond to pleas for help from aid workers under attack in a nearby hotel compound.
The fierce fighting in Juba involved helicopter gunships and tanks pitting President Salva Kiir's government forces against those loyal to ex-rebel chief Riek Machar.
Russian Deputy Ambassador Petr Iliichev criticized the decision to sack Ondieki as "premature" and said it should be reconsidered.
But UN peackeeping chief Herve Ladsous told reporters after a council meeting that the report's "conclusions were irrefutable" in detailing the force commander's failings.
The Kenyan ambassador insisted there was a "systemic failure" at the United Nations and that responsibility lay also with the department of peacekeeping in New York and the joint command of the UN mission in Juba.
The UN spokesman however said in response that Ban has "full confidence" in Ladsous, of France.
The 16,000-strong UN mission known as UNMISS has been deployed in South Sudan since its independence in 2011 and it has been sheltering civilians at designated sites since the war broke out December 2013.