Johnson, on sick leave due to a stress-related illness, has opted to stand down from his position.
His resignation follows allegations of financial misconduct which were brought to the Otago Cricket Association's notice late last month.
OCA chief executive Ross Dykes said, the nature of the complaint represented a serious breach of trust.
"The association was made aware of an allegation involving Mr Johnson and raised it with him. It has since accepted his resignation,'' Dykes said.
"This has been a very sad and disappointing episode for all concerned.''
Johnson issued a statement in which he apologised for his conduct.
"I have made some very bad decisions around my personal finances which have compounded to a point where I have let down Otago cricket and myself, Johnson said.
"I sincerely regret my actions and must now concentrate on restoring my health so I can do my best to make amends.''
Johnson (53) took stress leave early this month.
He had been Otago coach since June 2011 and last year signed on for two more years.
Dunedin-born Johnson, a former seam bowler who took 64 wickets in 27 first-class games for the province, and played 20 one-day games, had been in his second coaching stint at Otago.
He also spent 2000-06 as Wellington coach and has filled coaching roles with New Zealand Cricket since the early 2000s.
- Staff reporter/NZ Herald
