The former Youth Fund boss was found dead in her apartment.
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Ms Namuye collapsed and died at her home in Kileleshwa on Wednesday, Nairobi police boss Japhet Koome said.
Mr Koome said neighbours called the police after they heard people screaming from Ms Namuye's house at 11am.
She was pronounced dead at home by medics, Mr Koome said.
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The police boss added that police and medics who attended to her did not see any physical injuries on her body.
The body was taken to Lee Funeral Home awaiting a postmortem examination Mr Koome said.
Ms Namuye and former Youth Fund board chairman Bruce Adhiambo were last year charged with 12 counts of corruption in relation to the loss of Sh180 million of taxpayers' money.
The two were accused of receiving Sh6.3 million in kickbacks from Quorandum Ltd that prosecutors said “they had reasons to believe was corruptly acquired from the Youth Enterprise Development Fund.”
Ms Namuye was appointed CEO in July 2014 after holding the position in an acting capacity for more than a year.
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Her name featured in the Ethics and Anti-Corruption Commission dossier President Uhuru Kenyatta tabled in Parliament on March 26.
Despite being mentioned as under investigation for alleged malpractices, Ms Namuye continued discharging her duties as she did not step aside like her other Government colleagues, as directed by the Head of State.
Before her appointment to the Youth Fund she held the position of senior support manager at the NGO Consortium/NGO Security programme.
