The UN secretary general, Ban Ki-moon, has fired the head of the agency’s peacekeeping mission in Central African Republic after multiple sex abuse allegations against peacekeeping troops.

Ban pledged to take urgent action to weed out the “outrageous and indecent actions of a few people” as he announced the resignation of Babacar Gaye, from Senegal. “I cannot put into words how anguished, angered and ashamed I am by recurrent reports over the years of sexual exploitation and abuse by UN forces,” Ban said.

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The resignation, at Ban’s request, came hours after Amnesty International alleged that UN peacekeepers shot dead a 16-year-old boy and his father and raped a 12-year-old girl in two separate incidents on 2 and 3 August in CAR.

Those claims intensified pressure on the beleaguered UN mission in CAR, already under scrutiny over its recent handling of allegations of child sexual abuse by French soldiers and its own peacekeepers.

Ban has called a special session of the UN security council for Thursday over the issue of the sexual abuse allegations. He said: “When the United Nations deploys peacekeepers, we do so to protect the world’s most vulnerable people in the world’s most desperate places. I will not tolerate any action that causes people to replace trust with fear.

“Those who work for the United Nations must uphold our highest ideals. Yet the outrageous and indecent actions of a few people tarnishes the heroic work of tens of thousands of UN peacekeepers and personnel.”

Ban ordered an independent inquiry into the allegations in June and on Wednesday said he expected to receive their findings soon. “I believe the disturbing number of allegations we have seen in many countries – but particularly in CAR in the period before UN peacekeepers were deployed and since – speaks to the need to take action now,” he said. “Enough is enough.”

He described sexual exploitation as a “global scourge” and a “systematic problem that requires a systematic response”. Addressing victims of sexual violence, he said: “I want victims to know that we will strive to uphold our institutional responsibility to safeguard their security and dignity.

“To victims, I say we stand with you. Please come forward. Please feel safe in knowing that we will do all we can to respond to these outrageous crimes. You should not feel shame. Shame belongs to the perpetrators.”

Responding to news of Gaye’s resignation, Amnesty International’s senior crisis response adviser, Joanne Mariner, welcomed the “swift and emphatic response” to the allegations.

Mariner demanded an urgent investigation into the alleged incidents on 2 and 3 August in Bangui.

“The case we documented and others weren’t the first where there has been credible evidence against peacekeepers. The secretary general seems to be taking this very seriously and we’re happy to hear the strong language, of course, but what we need to see is a serious investigation into these allegations,” she told the Guardian.

The 12-year-old girl allegedly raped by a peacekeeper told Amnesty she had been hiding in a bathroom during a house search in a Muslim enclave of Bangui, on 2 August. A man allegedly wearing the blue helmet and vest of the UN peacekeeping forces took her outside and raped her behind a truck. She said that he dragged her out of the room, and slapped her when she started to cry. “When I cried, he slapped me hard and put his hand over my mouth,” the girl was quoted as saying by Amnesty.

She alleged that he brought her outside into a far corner of the courtyard behind a truck, groping her breasts and tearing her clothes. The girl later showed Amnesty her torn underwear and said: “He threw me to the ground and lay down on top of me.”

UN peacekeepers have been in CAR since September last year in an attempt to calm sectarian violence between Christians and Muslims which erupted after a coup in 2013.

He said he also will hold a special meeting on Thursday with the heads of all peacekeeping missions around the world to stress their responsibilities to “report allegations immediately, investigate thoroughly and act decisively”.

The resignation follows allegations that UN peacekeepers had sexually abused street children in Bangui and a separate allegation of child sexual abuse against a peacekeeper in the eastern part of the country.

The UN mission is also being investigated over how it handled child sexual abuse allegations against French troops last year.