The government took issue with cigarettes by British American Tobacco and Imperial Tobacco which carried ringed watermarks in their cigarette paper and batch codes which included references to travel destinations such as LDN for London, NYC for New York City and AUS for Australia.
Laws which come into force on Saturday strictly regulate the appearance and packaging of cigarettes.
A spokesman for Ms Plibersek said her department had met with the companies and told them it believed the alphanumeric codes and paper watermarks did not comply with the legislation.
The spokesman said the companies had agreed to change the codes and remove the watermarking.
''The government will not let 'Big Tobacco' get around the plain packaging rules,'' the spokesman said.
British American Tobacco spokesman Scott McIntyre said the company had contacted the health department as
soon as they were notified of the issue and had held discussions with it.
''We were very upfront about being more than happy to work with them for a mutually beneficial outcome,'' Mr McIntyre said.