"We see how day after day the government of Catalonia is pushing the population to the abyss and inciting rebellion in the streets," Juan Ignacio Zoido said, adding that his government would take "all measures necessary to stop acts of harassment".
Spanish national police have been driven out of their hotels in Catalonia by locals furious over police violence that marred the region's banned independence vote on Sunday, which separatist leaders organised despite strict orders from Madrid not to do so.
Hundreds of protesters gathered overnight outside a hotel in the seaside resort of Pineda de Mar, about 70 kilometres (40 miles) north of Barcelona where around 200 officers were staying.
In a letter shared on social media, the hotel management said it had asked police officers to leave the hotel after being "obliged" to do so by local authorities on pain of being shut down.
A further 200 members of Spanish special forces and riot police in Calella, a coastal city also to the north of Barcelona, were told on Monday they would be evicted.
Protestors also rallied outside police stations in Catalonia, according to Spain's main police union SUP.
On Sunday riot police moved in on polling stations across the region to stop people from voting in a referendum deemed unconstitutional by the Spanish courts.
Some officers ran baton charges and fired rubber bullets to disperse crowds.
SUP spokesman Ramon Cosio said the welfare of officers was now under threat.
"They are fleeing from hotel to hotel, they are like rats who have to hide," he said.
He added that the state was losing control of security.
Deputy Prime Minister Soraya Saenz de Santamaria branded the protests against police outside hotels and police stations "mafia behaviour".