Separately, financial documents show the social enterprise's chief executive Jim Duffy now receives an annual salary of £90,000, an increase from the £75,000 he originally received.
Much of the organisation's income comes from selling its services to public bodies such as councils.
It has received support from high-profile entrepreneurs like Sir Tom Hunter, Ann Gloag and Sir Willie Haughey and the likes of Royal Bank of Scotland, PwC, law firm Harper Macleod, Glasgow Caledonian University and Napier University.
An occupancy agreement, which those entering E-Spark had to sign, outlines what behaviour is acceptable with one of the clauses appearing to be designed to prevent criticism.
The document states: "Upon termination of this agreement the occupant agrees not to engage in any negative media whatsoever in respect of ES."
The clause also forbids the occupant from criticising the businesses which provides E-Spark's premises such as Sir Willie's City Refrigeration in Glasgow or Sir Tom's West Coast Capital in Ayrshire.
One entrepreneur who has experience of E-Spark, said: "There was a lot of unease about the [contract] but we didn't have a choice. We had to sign it or we wouldn't get in.
"People would talk about it but no-one would confront Jim [Duffy]."
ESpark, which had its work highlighted in a BBC documentary earlier this year, also has premises it uses in Edinburgh. A spokesperson for E-Spark: "The salaries of all staff, including the chief executive, are set independently by the E-Spark board which comprises Sir Tom Hunter and [Sir] Willie Haughey, two of Scotland's most highly regarded businessmen.
"These salaries are benchmarked against the sector and are deemed to be mid-range in respect to similar type organisations and entities. Success for any business or social investment must be measured by the return on investment.
"In its first year of operation, E-Spark has helped create 196 jobs and supported 139 start-ups with a combined turnover in excess of £3.5 million.
"In addition, more than 75% of E-Spark's funding comes from a mixture of corporate and private backing. We consult with our lawyers in creating the contracts we enter into with start-ups.
"We endeavour to ensure that the contracts we put in place are reasonable, in the context of what we are looking to achieve and the support and facilities offered."
The occupancy document also allows E-Spark to terminate the agreement with immediate effect and "remove the Occupant from the Work Space for any reason and without the right to appeal".
A further clause outlines mentors do not offer "professional advice".
It says: "ES holds no liability for advice given from any mentor.
"Occupants must be clear that mentors can offer guidance, but this is not, nor can it be ever claimed as professional advice.
"Occupants can therefore hold no mentor offered by ES liable for any detriment to their business as a result of guidance provided."
Mr Duffy has previously blogged on E-Spark's website about the need for the "privately led initiative with some local authority support" to be open and accountable.
Monthly management accounts posted online by the organisation show Mr Duffy's salary for 2013 has been set by the board at £90,000.
Sir Tom said: "In this world you get what you pay for. Jim has delivered well beyond the call of duty for E-Spark and in terms of value for money and return on investment, stands comparison to any other CEO I know."
Sir Willie said: "Jim Duffy has gone from managing two Hatcheries, to at present managing three and soon to be four. He now travels the length and breadth of the country, from Inverness to Ayrshire.
"He works between 60 and 70 hours a week, every week. Both myself and Sir Tom Hunter set Jim's wages after we benchmarked similar positions. For what it's worth, with his present workload and the outstanding successes he has produced, in my opinion he does not get paid enough."
The E-Spark accounts showed local authority income for the first half of 2013 had grown to £302,500, from £202,500 in the first half of 2012.
The accounts show all other income streams in the six months to the end of June were relatively static giving E-Spark an income of just short of £400,000.
Its largest expense was on wages and staff costs with £145,426 paid out in the half-year to the end of June, up from £119,190.
One E-Spark member said: "One speech Jim gave he said he wasn't in it for the money and could go to the private sector and get much more.
"Then we see in the accounts he is on £75,000 and has since then awarded himself a pay rise to £90,000. That really irked me."
Michael Hayes, founder of Scottish start-up meeting and advice portal Rookie- Oven, says he has heard concerns about the amount of time some E-Spark members are spending in the start-up phase without launching.
Mr Hayes confirmed he knew of others who are uncomfortable with the idea of signing non-disclosure style agreements and with the salary paid to Mr Duffy and said: "Those things are certainly being talked about."