In September the court had ordered Mas and eight other top Catalan officials to pay €4.8 million ($5.6 million) with interest of €400,000 to cover the expenses of the ballot, which was declared illegal by the Constitutional Court.
But they have managed to pay just €2.9 million so far, prompting the court to order the seizure of assets they had put up as a guarantee, a spokeswoman for the court said.
Besides Mas's Barcelona home, the court seized half of a home belonging to former Catalan government spokesman Francesc Homs in Taradell, near the Catalan capital, the spokeswoman said.
It also seized properties belonging to three former regional ministers in Mas's government.
Mas, Catalonia's president from 2010 to 2016, has said the order to repay the costs of the 2014 referendum lacks "any kind of legal basis" and is aimed at trying to "intimidate" separatists.
His successor, Carles Puigdemont, pushed ahead with a banned independence referendum in Catalonia on October 1st, which was marred by a violent police crackdown against voting, and which led the Catalan parliament to declare independence on October 27th.
Spain's central government subsequently dismissed Puigdemont's government, suspended Catalonia's autonomy and called an early election in the region for December 21st.
Puigdemont fled to Belgium at he end of October, fleeing charges sedition, rebellion and misuse of public funds over his government's independence drive.