The decision comes as axed Catalan leader Carles Puigdemont faces an extradition hearing in Belgium...
Six other former ministers who were also remanded in custody last month will be released on bail of 100,000 euros ($120,000) each as an investigation into charges of rebellion, sedition and misuse of public funds continues, the Madrid court said in a statement.
The decision comes as axed Catalan leader Carles Puigdemont faces an extradition hearing in Belgium, where he escaped to after his region's parliament declared independence on October 27, claiming he would not get a fair trial back home.
Spain is seeking to have Puigdemont and four of his former ministers who also fled with him sent back to face charges over their role in the independence drive.
News that Junqueras, former regional interior minister Joaquim Forn, and two civil society leaders will stay in prison comes as the official campaign for Catalan elections on December 21 kicks off at midnight.
Madrid called the polls after the independence declaration, sacked Catalonia's government and suspended the region's autonomy.
Supreme Court Judge Pablo Llarena decided there was a risk that Junqueras and the three others would repeat their alleged offences if he released them.
The news sparked outrage among independence supporters.
"We want you back home," tweeted Catalan parliament speaker Carme Forcadell, who is also under investigation over her role in Catalonia's secession drive.
"We will turn sadness into energy and we won't stop until you are free."
Madrid wants the elections to "restore normality" to the wealthy northeastern region, which declared independence unilaterally following a referendum that went ahead on October 1 despite a court ban.
Puigdemont, Junqueras and other former ministers are candidates for the elections.
This means the campaign will take an unprecedented turn, with candidates both "in exile" and in prison.
Separatist parties have repeatedly accused Madrid of taking "political prisoners" and "repression" after their independence declaration fell flat, and the decision to keep some Catalan leaders in jail is likely to magnify those claims.
But generally, Catalans remain deeply split on independence, and several polls suggest pro-secession parties might struggle to win enough seats to form a new regional government.
"From now until December 21, the dispute in the pro-independence camp is going to get worse and they will exchange blows," said Oriol Bartomeus, a political science professor at the Autonomous University of Barcelona.
"They could open up a rift that prevents them returning an overall majority."
In 2015 pro-independence parties won 47.8 percent of the vote, which allowed them to form the largest bloc in the region's parliament.
But the latest polls show support for secessionists hovering around 45 percent -- potentially putting another majority out of reach.
And unlike 2015, pro-independence parties are running on separate lists.
Junqueras hopes to lead his ERC party, which is ahead in the polls, to victory on December 21.
Puigdemont launched his campaign last month from Brussels with a flurry of high-profile media appearances and a demand that he be returned as the "legitimate" president of Catalonia.
After Monday's hearing the court is expected to make its ruling in eight to 10 days, according to the Brussels prosecutor's office.
But Puigdemont's lawyer said at the weekend he will remain in Belgium until after the Catalan elections, which indicates he will campaign from there.
"No matter what, they will be (in Brussels) till at least December 21 and according to my calculations this could go on till mid-January," lawyer Jaume Alonso Cuevillas told Catalan radio Rac1.
"I am convinced that no matter what happens they will have recourse to an appeal," the lawyer said.
Spanish Prime Minister Mariano Rajoy and fellow opponents of Catalan independence, meanwhile, have hitched their hopes on a record turnout on December 21 to return a legislature in favour of unity with Spain.