In the statement released on Friday evening, the Governor stated that he is yet to carefully consider the matter in view of the unexpected turn of events.
"The Governor Mike Mbuvi Sonko has received a letter of resignation from Deputy Governor Polycarp Igathe. The Governor is considering the letter and will issue a comprehensive statement later," the brief statement read.
Here is a copy of the statement from City Hall.
Speaking to Kenyans.co.ke, Governor Sonko's Communications Officer, Joab Mwaura, conveyed that the Governor was not aware that his deputy was planning the move.
"We learnt of his resignation through the media before receiving the letter. Mr Igathe had not indicated any discontentment before the events of today (Friday) which makes his decision a surprise.
"As stated, Governor Sonko will establish the facts and give his considered view as soon as possible," Mr Mwaura told Kenyans.co.ke.
The Deputy Governor indicated in his resignation letter that he had decided to quit the job because he had "failed to earn the trust of the Governor to enable me to drive admin and management of the county."
Mr Igathe also thanked the Governor for the opportunity while expressing a clear conscience and no hard feelings towards Sonko.
"Serving Kenyans, in Nairobi under your leadership, has been a high honour and distinct privilege. I am grateful to Nairobians and yourself for giving me the opportunity to serve. Thank you, and please accept my highest personal regards," his statement partly read.