Mr Milosovski said that in the meantime, security forces would not launch any fresh offensives until the deadline had expired at noon on Thursday, but they would respond "if provoked".
The government said the ultimatum - ordering the rebels to lay down their arms or leave the country - was a final warning.
The new administration - formed only last Thursday after days of wrangling - is attempting to stop the country being sucked into a civil war by the rebel campaign.
"This is the last deadline we are giving to the civilians to leave the villages and the terrorists to leave their positions," said government spokesman Antonio Milosovski.
"After this we will take adequate measures to finally eliminate the threat," he said.
Mr Milosovski said that in the meantime, security forces would not launch any fresh offensives until the deadline had expired at noon on Thursday, but they would respond "if provoked".
Macedonian forces have been shelling and firing on several rebel-held villages for the past fortnight, leaving thousands of civilians trapped.
Around 9,000 other civilians have fled across the border into neighbouring Kosovo.
The Macedonian army said it had killed 30 rebels during a massive operation on Saturday, but the militants have denied losing any fighters.
The new government's ultimatum comes a day after Prime Minister Ljubco Georgievski said he would crack down on the rebels, saying a "frontal assault" was under consideration.
BBC correspondents say the new government faces a difficult task in persuading the rebels to withdraw without more bloodshed, while striking a deal to improve relations between Macedonia's ethnic communities and preparing for new elections.
Macedonia's new defence minister, Vlado Buckovski, confirming that a policeman had been injured in a rebel attack, warned that instant peace was not likely.
"We must not bear any illusions that such attacks will halt overnight," Mr Buckovski said.
"The new government has no magic wand but we will work painstakingly to solve our country's problems."