South Ayrshire Council remains supportive and has committed £50,000 per year until 2015 to the E-Spark facility in Dundonald.
Meanwhile, the fact E-Spark asks members signing an occupancy document to agree "not to engage in any negative media whatsoever in respect of ES" resulted in a lot of debate on social media sites.
On LinkedIn Stuart McDonnell, managing director at The Plan Design and Manufacture, said: "I'm surprised that a forward looking set-up would require such measures.
"Best thing would be to have an explanation as to why this clause is required, from those responsible for creating it."
Lesley Bloomer, executive director for economy, neighbourhood and environment at South Ayrshire Council, said the authority has seen benfits from partnering with E-Spark.
She said: "Entrepreneurial Spark is an innovative approach to supporting start-up companies and creating sustainable jobs that is supported by all three Ayrshire Councils.
"It's a successful business model that is designed to make businesses work and deliver an increased number of jobs from new companies, which benefits local people and the local economy.
"Feedback on the intensive support it offers to start-ups has been very positive and we will continue to monitor its achievements closely to ensure it creates jobs and delivers for the Ayrshire economy on an ongoing basis."
High profile supporters Sir William Haughey and Sir Tom Hunter have reiterated their backing to E-Spark and its founder Jim Duffy.
Some members of E-Spark defended the incubator, with co-founder Brian McGuire using Twitter to say: "Jim Duffy 60 [hours] per week, one week holiday, 100% for 300 E-Spark start-ups! What have these detractors achieved?"
On LinkedIn, David Blockley of software company Integral Ecology, which is helped by E-Spark, suggested the clause was necessary and said: "It's a fair enough request to prevent some of the looneys [sic] and moaners who get accepted and then are looking to blame someone else (E-Spark) for their lack of success.
"Every business that goes through the E-Spark process and plays by the rules comes out the other side in better shape."