The problems have seen some users of the service -- dubbed 'iinetphone' -- unable to make or receive calls to and from the more traditional telephone services of other carriers like Hutchison and Optus.
In a response to customers complaining on broadband information site Whirlpool, iiNet senior systems engineer Paul Raj Khangure outlined the problems.
"As we head towards 2,000 users, we're starting to find out some of odd call scenarios which don't work," he wrote. "For example, someone in one call zone can call a Vodafone number, someone in another can't.
"Someone on an Optus line in one suburb can't call any iinetphone numbers, but someone on an Optus line in the next suburb has no problems".
Khangure told ZDNet Australia the problem was not caused by iiNet itself, or related to Internet telephony in general.
"The main challenge is not actually with our VoIP product but with other carriers that need to fully condition their networks so calls can be routed to our telephone numbers," he said.
"The same problem would occur if it were a new number range to be used for mobile phones, or dial-up Internet," he said. The Internet Service Provider is reporting each individual problem to the external carrier concerned.
Khangure said each carrier had to re-configure every single one of their telephone exchanges to handle the new iiNet call types. "It's a task of considerable magnitude," he added.
There is one particular carrier causing iiNet headaches, however.
"We had requested a large carrier to condition their network many months ago in preparation for our VoIP launch," said Khangure, adding iiNet had believed the carrier had complied with the request.
"However, due to the magnitude of the task, it appears that some parts of their network, especially in regional areas, were either not included in the conditioning process, or had issues with the routing changes," he said.
"As a result, calls from affected areas on that network do not have the appropriate routing information for the call to be sent to us.
"This also affects some smaller carriers who send their calls to that large carrier to deliver".
Khangure noted iiNet had lodged a fault notification with that specific carrier, but noted the problem could take 10 to 15 business days to fix.
It "has to be done very carefully to avoid them disrupting all calls on their network," he said.
Most of the complaints about the service posted by customers on Whirlpool relate to interconnection with mobile services from Vodafone, Virgin, Hutchison and Optus, as well as fixed line services from Optus.
iiNet staff posted online that staff from Hutchison were aware of the problem.
Khangure defended the overall quality of the service, pointing out iiNet's service was one of the largest so far to be launched.
"While this has created some short-term complexities, we are confident that our efforts will rewarded," he said.