Kiwomya joined the League One club as development squad manager in February last year, but took over the first team following the departure of Keith Curle.
County have had a poor start to the season, winning just two of their opening 13 league matches, and the 1-0 defeat at home to Preston was the last straw.
Steve Hodge - Kiwomya's successor as development squad boss - has been put in temporary charge.
Chief Executive Jim Rodwell told the club's website: "I cannot express how difficult a decision that this has been for the Board of Directors.
"This has been a grueling year for Chris, both on the pitch and personally. Chris has conducted himself with dignity and professionalism throughout.
"We would like to state, for the record, that we continue to hold Chris in high regard. His work rate, enthusiasm, commitment to the club and importantly, honesty and integrity are commodities rare in football today.
"We put our faith in Chris towards the end of last season and genuinely thought that we had found the man to bring stability and a long-term vision to the manager's role here at Notts.
"However, it simply hasn't worked out how we had envisaged and unfortunately, as we all know, this is a results driven business and there has to be a line that we simply cannot cross. Chris has a real talent for spotting and nurturing young talent that I am confident will serve him well in his career.
"As a board it is our responsibility to look after the best interests of the club at all times and above all else, which is why we felt obliged to agree to go our separate ways, but Chris can be proud of his time at Meadow Lane and with a little more luck I honestly believe things could have been very different."
Two of Kiwomya's staff, Mick Jones and Andy Watson, have also departed.