Mr Bowles as he appears on the council's website
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Union leaders in Lincolnshire say the departure of a top council official means staff may be afraid to speak out.
Chief Executive David Bowles is leaving Lincs County Council after tension between him and senior politicians.
Unison spokesman John Sharman said employees might be reluctant to whistle blow.
Mr Bowles testified at the trial of former council leader Jim Speechley, who was convicted of misconduct in public office.
Mr Bowles is leaving under a deal that could cost the council up to £400,000.
'Some difficulties'
Mr Sharman said: "There is a sense that we have a culture that does not support people who whistle blow or stand out for the truth."
The union has asked the district auditor to look at the case to see why so much money is being used to get rid of "a perfectly good public servant".
"He (Mr Bowles) is highly respected and has been forced out of office - he has been victimised.
"The money spent on this is needed for public services," Mr Sharman said.
The council's new leader Ian Croft has said he is sorry to see Mr Bowles leave, but council officials have said there have been "difficulties between the pair".
Mr Sharman said: "People have said to me: 'If the bloke at the top can get the chop for blowing the whistle - if we are encouraged to speak out against bad practice - what confidence can we have that the organisation is going to deal with what we say properly.
"They are saying: 'What promise do we have that we will be protected for having the courage to stand up?'"
"There is a sense of anger and injustice."
Mr Bowles told BBC Radio Lincolnshire: "I am highly professional and have worked in local government for 20 years with people of different political persuasion.
"But if the other person is not prepared to work with you, then you have no alternative."