It is the most serious threat Rajoy has made since Catalonia held an independence referendum on October 1, triggering Spain's worst political crisis in decades.
Madrid dismissed the vote as illegal but Catalan leaders saw it as a mandate to announce a split from the country.
On Sunday, Spanish Foreign Minister Alfonso Dastis gave a glimpse into what Catalonia under direct rule might look like.
"We are going to establish the authorities who are going to rule the day-to-day affairs of Catalonia according to the Catalan laws and norms," he told the BBC's Andrew Marr.
He called on the Catalan people to ignore the current regional authorities, including the police, once Madrid declared direct rule and said that new elections should bring in new leaders.
"They wont have any legal authority, so they will be equal to a group of rebels trying to impose their own arbitrariness on the people of Catalonia," he said.
He said that the regional police could resume their duties once they had been placed under the authority of Madrid or newly elected Catalan leaders.
Dastis denied that Madrid would need to send in large numbers of police or the military to impose direct rule.
"We hope the regional police, once put under the control of people who respect and who uphold the Catalan rules and Spanish rules, everything will be fine."
'Attack on democracy'
On Saturday, nearly half a million people protested in Barcelona, Catalonia's biggest city.
Demonstrators shouted "Freedom! Freedom! Freedom!" and "Rajoy, Rajoy, so you know we are leaving!"
Catalan President Carles Puigdemont was among the throngs, but he stopped short of declaring independence, as he had threatened to do earlier in the week.
"The Catalan institutions and the people of Catalonia cannot accept this attack," he said later in a televised statement, accusing Madrid of seeking the "humiliation" of the Catalan people.
"What is being done with Catalonia is directly an attack on democracy that opens the door to other abuses of the same kind anywhere, not just in Catalonia."
Other Catalan politicians were similarly defiant. Catalan parliamentary leader Carme Forcadell accused Rajoy of "enormous political irresponsibility" that "trespassed all limits."
"He announced a de facto coup d'etat with which he aims to take over Catalan institutions," Forcadell said Saturday.
"We will not take a step back. We were chosen by the people of this country as legitimate representatives, and as public servants we owe ourselves to them."
Rajoy calls for new elections
Rajoy is seeking to employ Article 155
of the constitution, which would allow the national government to suspend the autonomy of the Catalan regional administration. Rajoy said the measure would be sent to the Spanish Senate within the week.
New elections should be called for Catalonia within six months, Rajoy said, adding that he wants it to happen as soon as possible.
Under the measures proposed Saturday by Rajoy, Puigdemont, his vice president and ministers would be suspended and replaced by the administration in Madrid, where necessary.
"The government had to enforce Article 155. It wasn't our desire, nor our intention. It never was," Rajoy said. "But in this situation, no government of any democratic country can accept that the law is ignored."
In undertaking these steps, the government has four goals, Rajoy said -- to return to legality; to restore normality and coexistence in Catalonia; to continue the region's economic recovery; and to hold elections under normal conditions.
Spain's FM denies excessive use of force
Catalan media reacted Sunday to Rajoy's announcement with editorials goading Puigdemont to declare independence soon.
The Catalan daily Diari Ara published photos of the march under the banner "Freedom," while the daily El Punt Avui showed a photo of Rajoy in black and white overlooking the colorful protests under a the headline: "Returning to the past." It also ran an editorial under the headline: "An unacceptable attack."
Every move Madrid has made to ward off an independence declaration, the Catalan people appear to have responded to with more vigor.
Madrid sent thousands of police into Catalonia to stop the October 1 vote, but officers were seen using what many called excessive force, shooting rubber bullets at protesters, dragging voters from polling stations by their hair and restraining elderly people.
Even though members of the Spanish government eventually apologized for the police's force that day, Dastis defended the police Sunday, saying that the use of force was "limited" and "provoked," and that many of the images had been doctored and constituted "fake news."
Implications of independence
Nearly 7.5 million people live in Catalonia, an economic powerhouse in the northeast of Spain. Spain's population is almost 49 million.
More than 2.25 million people turned out to vote, with the regional government reporting that 90% of voters favored a split from Madrid. But the turnout was low -- around 43% of the voter roll -- which Catalan officials blamed on the central government's efforts to stop the referendum.
An independent Catalonia would be outside the European Union and its single market, which is essentially a free-trade zone.
EU leaders have backed the Madrid government in its handling of the crisis, which Rajoy insists is an internal matter.
Catalonia would also sit outside the World Trade Organization, which could have consequences for the region's economic health.
Amid the uncertainty, businesses have already started to move their legal headquarters out of Catalonia.
According to a tweet Friday by the National Association of Registers, 1,185 companies began that process between October 2 and 19.