Harris was known across Latin America a children's champion
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Central America's main children rights group has sacked its UK-born director, saying he had "acted incorrectly" with a boy the organisation had once helped.
The group, Casa Alianza, said Bruce Harris had admitted paying for sex with a 19-year-old Honduran who had been a resident in one of its shelters.
Mr Harris has not commented directly, since he announced on Thursday he was resigning "for personal reasons".
But he has said he would co-operate with prosecutors in Honduras.
"Sheltering behind a lie has never been my way, so I assume, as I always have done, responsibility for my acts,
correct or incorrect," he said.
He had earlier issued a statement saying he was resigning to spend more time with his family.
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Covenant House has dismissed Mr Harris because he recently paid a 19-year-old Honduran boy for sexual favours in a
Tegucigalpa motel
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But Casa Alianza says he had an recent encounter with the teenager in a hotel room in the Honduran capital, Tegucigalpa.
"The young man
had been a Casa Alianza resident until the end of 2002," said the statement.
"We're a child care agency, our primary concern has to be the good of the children," said a spokesman for Casa Alianza's parent-organisation in the US, Covenant House.
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While we all try to do our best,
we are also human
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In 15 years working for the group, Mr Harris became well-known in Latin America as a vocal campaigner for the rights of street children.
He was awarded the Order of the British Empire medal in 2000 for his work.
A recent UK documentary showed him combating child prostitution in Costa Rica - where he is based - including working undercover in a child brothel to gather evidence.
"Some will be happy to see my departure," said Mr Harris.
"I am very sorry if I have disappointed anyone for this or other
decisions I have taken," he said. "While we all try to do our best,
we are also human."