The planning authority's audit officer, Joseph Falzon is considering stepping down because he "cannot continue working in such a hostile environment".
"I haven't yet decided whether I will be resigning but I'm thinking about it. All this (my work) is a waste of time," Mr Falzon said.
In less than a week, Mr Falzon's actions were harshly condemned and criticised from two fronts: by Prime Minister Lawrence Gonzi, who accused him of jumping to conclusions on Sunday, and, four days later, by the Malta Environment and Planning Authority.
Mepa lashed out at its own auditor over a report probing a development permit in Qala, saying he should never even have investigated or published the report because the matter was still before the appeals board. It said Mr Falzon's actions contradicted the Ombudsman decision, a higher institution.
A similar situation arose in 2008 when, on Mepa's request, the Ombudsman told Mr Falzon that publishing a report on the controversial recycling plant in Marsascala would prejudice the pending appeal. Mr Falzon had complied.
This time, Mr Falzon criticised a decision by one of Mepa's boards that allowed a hotel overlooking the picturesque Mġarr harbour to be converted into apartments, saying this permit should never have been granted.
Mepa's criticism was the last straw for Mr Falzon who said. "Whenever I criticise something, everyone goes on the defensive. If the authorities don't want an auditing process then why don't they scrap it, after all it's costing the country millions of euros?"
Regardless of Mepa's criticism, Mr Falzon still felt he did the right thing in looking into the case because of its environmental importance. "I decided to investigate the case because an appeal was filed by a third party. This meant the developer could go ahead with his works because he had all the permits in hand," he said.
If, and when, the board decided in the objectors' favour, it would have been too late because the development would have materialised, he added.
Mr Falzon criticised the workings of the appeals' board, which, he said, took an exaggeratedly long time to decide, sometimes years. The appeals' board was not a useful tool for third party objectors, he insisted.
He said there was nothing in Mepa's regulations preventing him from investigating a case under appeal.
Mepa's criticism and the Prime Minister's comments led Mr Falzon to describe his situation as "intolerable".
"The role of an auditor is there for a reason: to point out an organisation's shortcomings," he said.
Dr Gonzi described Mr Falzon's comments on a court ruling as "shameful" because he had not asked for explanations but just jumped to conclusions. However, when contacted earlier this week, Dr Gonzi said he would not be demanding Mr Falzon's resignation.
Mr Falzon's comments were on the controversial Mistra disco development case after a magistrate cleared two former members of the Developement Control Commission of exercising private interests in approving the outline permit for the open-air disco.
The magistrate concluded that meetings between planning board members and developers were common practice.
Mr Falzon deems such meetings "illegal"", even though he acknowledged the magistrate was making a statement of fact when she said such meetings had become common practice.
Meanwhile, Labour environment spokesman Roderick Galdes said the auditor's report confirmed the Qala development was not consistent with the area's policies.
Mr Galdes, who is also Labour's representative on the Mepa board, said the auditor should be allowed to continue checking the accountability and transparency of the planning process.
Similarly, the Ramblers Association said it was shocked by Mepa's rebuke and insisted an explanation was morally due.