In a press conference, Carles Puigdemont said the regional ministers in charge of interior matters and education, as well as government spokeswoman Neus Munte -- all three on the front line in the organisation of the referendum -- had "decided to step aside".
He did not give a reason for their departure, but Catalonia's executive has recently been hit by internal divisions over the vote planned for October 1st as Madrid ups pressure on members of the separatist regional government.
The first public sign of tensions came earlier this month when Jordi Baiget, the regional councillor in charge of business, expressed doubt over whether the referendum could take place, given the power of Madrid.
Madrid has remained steadfast in its opposition to such a vote, considering it a threat to Spain's unity.
The Constitutional Court has already quashed a resolution approved by Catalonia's parliament calling for the referendum to take place.
It has also warned Catalonia's elected officials that they will face legal consequences if they take any steps towards holding such a vote.
But Baiget's comment was not to the liking of Puigdemont, who promptly announced his departure -- a decision that was criticised by some of the most fervent supporters of independence.
Then this week, cracks emerged between Puigdemont and his number two Oriol Junqueras, who has refused to be put in charge of organising a referendum -- as wanted by his boss -- and would rather the entire executive take the responsibility of such a controversial vote.