Media companies will not be told if their journalists' communications records are being accessed via warrant, sparking fears the protections will be no more than a "tick and flick formality" that will have a "chilling effect" on press freedom.

The government and Labor have agreed to amend controversial new metadata laws after a fierce backlash from media companies amid concerns it could lead to journalists and their sources being targeted.

Attorney-General George Brandis said on Tuesday the government had only agreed to the "entirely unnecessary" extra protections of requiring a warrant for access in the case of journalists to address "red herrings" raised by the Greens and the journalists union.

The laws, set to be passed by the end of next week will require telco companies to keep customers' communication logs for two years from 2017.