In a letter to UN Secretary General Ban Ki-moon, Mr Pachauri said he was unable to provide strong leadership.
Indian police are investigating a complaint from a 29-year-old woman working in his office in Delhi.
Lawyers for the woman say the harassment included unwanted emails as well as text and phone messages. Mr Pachauri has denied the allegations.
Mr Pachauri, who had chaired the IPCC since 2002 and whose second term was due to end in October this year, denies any wrongdoing and says his email account and mobile phone were hacked.
His office at the Energy and Resources Institute in Delhi (TERI) said he had gone on "long leave" from the organisation.
On Monday, the 74-year-old had pulled out of a high-level IPCC meeting in Kenya starting on Tuesday, because of "issues demanding his attention in India", an IPCC spokesman said.
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