Customers from major Internet service providers, including Telstra, Optus and Vodafone, were unable to access the Melbourne Free University website for nine days.
The convenors of the organisation, which hosts free public lectures, were told by their ISP that it could not reveal why their website was blocked or who blocked it.
"Clearly ASIC have an issue with how they went about it -- mistakes were made and we've got make sure that we have proper transparency and oversight," Conroy said.
Conroy denied the use of section 313 was a back door way of implementing an Internet filter, with the controversial ISP-level Internet filter scheme abandoned by Conroy late last year.
Instead of the filter, the Federal Government indicated it would seek to use section 313 to block child abuse websites listed by Interpol, with participation by ISPs voluntary.
"Complying with existing laws is not a back door way of doing anything," Conroy said. "My department is not involved in any other activity in this area."
A broader range of sites would have been filtered under the government's nixed 'clean feed' scheme, but Conroy said he was "comfortable" with the current arrangement of only blocking Interpol-listed websites.
"We set out to ensure that Australian's couldn't stumble across or find particularly vile pages that involved child abuse," Conroy said. "I'm very comfortable with where we've finished up."
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