He is expected to start his new job in the Nigerian capital Abuja in January.
Admire Masenda, the President of the ZOC, admitted that Mutsauki is a big loss to their organisation.
"It's a significant loss because Robert Mutsauki has made immense contribution to ZOC," said Masenda.
"He has been in the driving seat, pushing ZOC to where it is today.
"It is a very sad loss."
Mutsauki, 51, first joined the ZOC as one of its two vice-presidents in April 1998.
In that time Zimbabwe have claimed a total of Olympic seven medals, two of them gold, all won by swimmer Kirsty Coventry (pictured).
As head of the technical team, Mutsauki had helped the continental ANOCA to successfully host the inaugural African Youth Games in Rabat, Morocco, in July.
"As you know, I was working with them [ANOCA] on a part-time basis which effectively means I was carrying out Anoca duties from time to time including the organisation of the inaugural African Youth Games in Morocco in July," said Mutsauki.
"And last month I travelled to Maputo, Mozambique, to inspect the facilities for next year's All-Africa Games which will run from September 3-18.
"At the ANOCA headquarters in Abuja there are currently three full-time staff members and I'm going to be the fourth one and I'll be running my own department."
Mutsauki will also provide support and guidance to African National Olympic Committees on Games team preparations and management, including for London 2012.
The search for a replacement at the ZOC is expected to start next month.
"One thing we have is that we have been able to put in place systems that will enable us to continue beyond his departure," said Masenda.
"Our next board meeting is on around the 17 of December and that is when we will sit as a board and chat the way forward.
"We have begun discussing the options.
"There are no names yet but we have options to look from within and outside ZOC."