The 25-year-old unnamed maid filed a complaint with police last month accusing Dr Yonas Tegegn, the WHO's representative in Thailand, and his wife of abusing her and forcing her to work without pay for nearly two years.
Police on Wednesday said they would investigate the allegations and question the couple, who are also Ethiopian nationals.
In a statement released today, Tegegn denied the claims.
"These accusations made against me and my family are baseless. We deny any wrongdoing," he said in a statement emailed to AFP.
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The unnamed maid's lawyer Surapong Kongchantuk from the Lawyers Council of Thailand told AFP earlier in the week that she had worked for the family between July 2013 and March this year.
He alleged that she had not received a proper salary during that time, had to sleep in a room with the family's dog, was physically abused and was only fed rice.
He said the maid escaped her employers when she was rescued by passers-by after a suicide attempt and is being helped by a local NGO to pursue a case against her employers.
"After that date she was scheduled to return to her home country Ethiopia," the statement said.
Tegegn added that "at all times we have treated her (the maid) as a member of our family, with all dignity, respect and consideration".
A WHO official in Bangkok said the organisation was "aware of the allegations in the media about a private matter between Dr Yonas and his former employee".
"WHO is taking this allegations very seriously, and we are reviewing them according to WHO internal procedures," the spokesman said.