"The role of the NSWEC has changed considerably in recent years," the report says.
"No longer can it be characterised as a 'boom and bust' organisation that experiences long periods of dormancy punctuated every two years by frenetic activity that is associated with state government elections or a suite of local government elections."
It warns that with the commission's "expanded and broadened" remit, its funding model has not changed and is based around "election events" rather than ongoing work, including compliance and enforcement around political donations.
"As a consequence of the of its current funding model, the NSWEC has a high-cost employment model and a highly transient workforce," the report says.
"Relatively few people are employed on an ongoing basis and the organisation relies heavily on a contractor pool who cost significantly more per head."
It says an "inadequacy in baseline funding" has meant there is an under-investment in staff training and the staff profile is "characterised by fragility".
The document, prepared earlier this year but tabled in last month's estimates hearing, warned that 60 per cent of the roles "identified as critical" cannot be guaranteed without more funding.
"Relatively few people are employed on an ongoing basis and the organisation relies heavily on a contractor pool who cost significantly more per head."
NSW Electoral Commission internal report
The electoral commissioner John Schmidt told last month's budget estimates hearing that the agency received $82 million to run this year's election, $30 million more than for the 2015 poll.
But Mr Schmidt said he had asked several times for funding increases for the commission's other work, particularly in light of an increased requirement on compliance around political donations, but was not successful.
A spokeswoman for the commission said: "The Electoral Commissioner remains concerned about the NSW Electoral Commission’s (NSWEC) funding model.
"The NSWEC is in communication with the Department of Premier and Cabinet regarding this matter."
A spokeswoman for the Premier said annual funding for special offices, including the NSW Electoral Commission, is "specifically approved by Parliament under the Appropriations Act".
"The NSW Electoral Commission received $121.9 million in the 2019-20 NSW Budget. This year’s funding reflects the cyclical budget with no major election to be held in 2019-20," the spokeswoman said.
In response to questions on notice raised in budget estimates, the Premier's office said the government was "committed to ensuring the highest level of integrity in all electoral matters by supporting the independent NSW Electoral Commission’s work".
"The Electoral Commissioner recently indicated his satisfaction with the funding for the 2019 State
general election, noting that it was a significant increase in funding from the 2015 election."
Labor's leader in the upper house Adam Searle, said the government was "creating a risk to the integrity of electoral outcomes" and "compromising the ability of the independent Electoral Commission to properly supervise electoral funding and disclosure laws".
Alexandra Smith is the State Political Editor of The Sydney Morning Herald.