Ministers are trying to shift the blame for failing policies on to civil servants, the leader of the union for top Whitehall officials has said.
Mr Reid said parts of the Home Office were 'not fit for purpose'
In a BBC interview, Jonathan Baume, general Secretary of the First Division Association, cited recent problems with immigration and foreign prisoners.
Ministers' behaviour had been "unfair" and "cowardly", he said elsewhere.
But Home Secretary John Reid and the Home Office's top civil servant said they had "complete unity of purpose".
Mr Reid had to apologise to MPs last month for giving them the wrong figures on foreign prisoners.
He warned that all statistics he provided should come with a "health warning" because he had found Home Office information always seemed liable to change.
Mr Reid also said the department's immigration operation was "not fit for purpose" and that jobs could go after 1,019 foreign prisoners were released without deportation being considered.
In an interview for BBC Radio 4's Westminster Hour, to be broadcast on Sunday, Mr Baume criticised the government's handling of the Home Office situation.
In a separate statement, he said: "Some recent criticism of the civil service looks like an ill-disguised attempt by some politicians and commentators to make excuses, and shift responsibility for struggling policies from ministers to the staff who serve them."
He called it "absolute nonsense" to suggest officials were not accountable for their actions.
Mr Baume also said: "The civil service must take it on the chin when it fails, and some criticism is justified. Nor should we shy away from debate on difficult issues.
"But creating scapegoats when a wider problem emerges is no solution. It only erodes credibility of the workings of government and destroys morale."
Home Office Permanent Secretary Sir David Normington and Mr Reid said in a joint statement: "There is complete unity of purpose between ministers and top officials in the Home Office to change the system to give the public the service they deserve.
"We share the analysis of the problem and the desire to lead the change needed."
Mr Baume later said he welcomed this "positive statement", adding: "We fully accept that there are problems to resolve in areas of the department.
"We will do all we can to facilitate the department's desired changes."
Mr Reid took over as home secretary last month after Charles Clarke was sacked amid the row over the release of foreign prisoners.