The 39-year-old former mayor of Florence will not be assured of a majority in the Senate without the 13 defectors and their absence will make it extremely difficult for him to push through legislation.
Mr Renzi's plan to abolish the Senate as an elected chamber in order to streamline the passage of legislation, set out when he took office in February, has been held up in the Senate Constitutional Affairs Committee. This week, Mr Renzi removed two PD opponents of the plan from the committee.
In a shock response, 13 PD senators said they were "suspending themselves" from the party, accused Mr Renzi of authoritarian tactics at odds with the constitution and said they wanted an open discussion with the prime minister.
Giuseppe Civati, a PD deputy frequently critical of Mr Renzi, said his removal of the senators from the committee was "a political error" and rebuked him for trying to "eliminate dissent" in the party.
The senators did not say they would leave the PD itself and their action was seen more of a warning shot to Mr Renzi than an immediate threat to his government's survival.