Mr Keogh's resignation takes effect today despite his five-year contract not expiring until June.
When contacted by the Otago Daily Times, Mr Keogh said he was unable to comment because of the terms of the agreement reached between himself and the council. He said he planned to move to Dunedin to join family there and was looking forward to trying new things.
The Local Government Act requires authorities to review chief executives' contracts six months before the contracts expire. Councils can extend a chief executive's contract by two years, or not renew the contract and advertise for a replacement.
In December, Environment Southland decided not to renew Mr Keogh's contract, prompting him to file a personal grievance against the council. Earlier last month, the council held a public-excluded meeting to discuss the grievance and the 10 councillors who attended unanimously decided to seek legal advice before taking any further action.
In a statement yesterday, Environment Southland chairwoman Ali Timms said the parties had resolved all matters in relation to Mr Keogh's employment to their "mutual satisfaction". She said the council recognised Mr Keogh had made a significant contribution to Environment Southland and understood he intended to pursue "other interests".
Mr Keogh took up his position with Environment Southland in 2007. He was also one of three candidates shortlisted for the chief executive position of the Christchurch City Council last year.