"No other agency should be involved in determining how members deal with information they hold ... equally, it is important that Members are able to communicate securely, safe from external cyber threats."
Carter said he agreed it was important MPs were able to communicate without hindrance but their emails also had to be safe from cyber threats. Finding that middle ground would be complex and he would work with parties on it.
The system at Parliament was primarily designed to protect confidential information in ministers' offices and Government departments so blocked attempts to send sensitive documents to non-approved emails.
Carter proposed a range of solutions, ranging from MPs manually removing classified elements to scrapping the system altogether - but said that create cyber security risks.
Hipkins said Carter's solutions did not resolve the problem.
"I was disappointed. The ruling means the firewall basically stays in place and the Speaker's suggestion we edit our emails to remove sensitive information isn't acceptable."
He said the system was designed to protect the Government and should not prevent Opposition or backbench MPs being able to send and receive information which could be damaging to the Government, such as information from whistleblowers.
Hipkins' concerns were echoed by other MPs, including United Future leader Peter Dunne whose email and phone data were provided to a 2013 inquiry into an information leak, prompting a Privileges Committee censure of Parliamentary Services' handling of information.
NZ First leader Winston Peters said it was an "outrage" such a system was being used across all MPs and showed little recognition of the role of MPs.
Parliamentary Service said the SEEMail encrypted email system used at Parliament was primarily to protect Ministers and Government departments which needed secure, encrypted email systems.
However it was in place for all Parliament addresses - including staff, Opposition and backbench MPs.
The filters looked for words such as "restricted, sensitive, confidential or 'SeeMail' and blocked emails unless they were going to another SeeMail e-mail address.
In a statement, a spokesperson for Parliamentary Service said the SEEMail system had been in place since 2007 and was aimed at allowing sensitive information to be sent "without compromise."
"We have over 14 million emails passing through our systems every year and we do not review messages manually, and nor do we want to - that is not our role at Parliament."
She said appropriate security had to be provided.
"Members are free to send and receive information as they choose and that has not changed."
In 2013 the Privileges Committee criticised Parliamentary Service for handing email and phone data of United Future leader Peter Dunne and journalist Andrea Vance over to an inquiry investigating the leak of a report on the GCSB.