The demonstrators want Mr Najib to face charges over allegations that billions were looted from his brainchild investment fund, 1MDB.
They were undeterred by a police ban and the arrest of a number of activists ahead of the planned action.
Mr Najib has denied any wrongdoing and says he will not be cowed by protests.
In a statement on his blog, Mr Najib called Bersih - the electoral reformist group which organised the protest - "deceitful". He said the group had become a tool for opposition parties to unseat a democratically elected government.