Critics said the original line-up showed Mr Mnangagwa had no plans to bring real change to the country despite hailing a "new democracy".
The education and labour ministers have now been replaced, ostensibly to comply with a constitutional provision.
But military chiefs remain in charge of the foreign affairs and land portfolios.
Ten days ago Mr Mnangagwa returned from exile following the military coup against Robert Mugabe, promising to serve all citizens equally.