The Pope did not cite the government by name, but in his address in Havana, he urged Cuban authorities to let the church more freely preach its message and educate its young in the faith in schools and universities.
The remarks came before Benedict's eagerly anticipated meeting with Fidel Castro.
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The 53-year-old was killed shortly after leaving her home in Mosta, Prime Minister Joseph Muscat said.
Jordi Sanchez of the Catalan National Assembly and Jordi Cuixart of the Omnium Cultural group were jailed on Monday.
Storm Ophelia continues to bring strong winds to western parts.