MADRID — The Spanish government has given a new ultimatum to Catalonia’s separatist leader to clarify whether he was withdrawing his plan to declare independence from Spain, after a Monday morning deadline for the separatists to make their intentions clear came and went.

After a perplexing speech last Tuesday before Catalonia’s Parliament, Carles Puigdemont, the region’s leader, sent a letter to Prime Minister Mariano Rajoy asking to negotiate a solution but declining to clarify whether independence had been declared.

“Mr. Puigdemont has a serious problem, not only in terms of respecting legality but also respecting citizens who are asking for clarity,” Soraya Sáenz de Santamaría, the deputy prime minister of Spain, said at a news conference in Madrid shortly after receiving Mr. Puigdemont’s letter.

The Catalan leader “should respond yes or no” by Thursday, she said. “It’s in his hands to avoid that the next steps be taken,” she said, although she would not detail how Madrid might use the emergency measures at its disposal if Mr. Puigdemont refused.