The prime minister stated the situation with the declaration of independence must be clarified before any step is taken under Article 155 of the constitution, which allows the central government to meddle in the affairs of its autonomous regions.
The ultimatum comes with a deadline: Catalonia has five days for the first demand, and another three days for the second, Reuters reports.
Thus Catalonia finds itself in constitutional limbo, as the Spanish Government announces it has requested clarification on whether or not the Catalan Government has actually declared independence.
National police were involved in violent scenes as they tried to stop the vote taking place.
While Catalan authorities say just under 90% of voters backed independence, turnout was only 43%.
It was a very intentional middle ground - not quite a declaration of independence, but something very close.
Marc Cazes, a student in Barcelona, said: "I did not expect independence to be declared today because of all the processes that the government of Spain has begun, both with police actions and with threats". "He was frustrated with what he heard last night".
Spain's Deputy Prime Minister Soraya Saenz de Santamaria described Puigdemont as someone "who does not know where he is, where he's going".
Formal confirmation from Barcelona is required to invoke Article 155 of the Spanish constitution, Rajoy said.
Prime Minister Mariano Rajoy will chair an emergency cabinet meeting a day after Catalan leader Carles Puigdemont signed a suspended declaration of independence and called for negotiations with Madrid.
Speaking to CNN on Wednesday, Catalan President Puigdemont explained that he had taken this position in order to comply with global requests for peaceful dialogue. "We are normal people who ask to be allowed to vote and who have been ready for all the dialogue necessary to achieve it in an agreed way".
But he proposed that the regional parliament of the wealthy region should suspend the effects of the declaration to commence a dialogue and help reduce tension, in what is Spain's worst political crisis in decades.
Rajoy gave Puigdemont until Monday to clarify whether the declaration of independence is real - and, if it is, until October 19, eight days from now, to either back down or be deposed.
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