Barca announced on Wednesday that Villanova needed a second round of surgery following an operation to remove a tumour in November 2011.
The latest procedure would be followed by chemotherapy and radiotherapy over the next six weeks and Roura would step in until Vilanova was well enough to return, the club said.
In a brief statement on their website on Thursday, Barca said Vilanova's progress would determine how long he remained in hospital but it was likely to be the three or four days originally expected.
The 44-year-old was sidelined for around three weeks after the surgery last year before returning to his job as assistant to Pep Guardiola and then taking over from his close friend at the end of last season.
Under his leadership, Barca have made a record-breaking start to their La Liga campaign and top the standings with a nine-point lead over second-placed Atletico Madrid.
They have dropped only two points in 16 matches - in a 2-2 draw at home to champions Real Madrid - and are 13 points ahead of their arch-rivals in third.
Barca are also through to the last 16 of the Champions League and were drawn on Thursday to play AC Milan when the competition resumes in February.
Club captain Carles Puyol said Vilanova had been able to reassure the players at a meeting on Wednesday and predicted there would be continuity under Roura, a graduate of the club's youth academy who was one of Guardiola's technical team.
"He [Roura] has been working with us for many years," Puyol told a news conference after Thursday's training.
"He is someone who is very active in the training sessions and our way of playing and tactics will not change," the Spain defender added.
"We are in good hands. It is the best decision to have put him in charge at this time."
All the players could do was keep playing the same way, train hard and wait for Vilanova to return, he said.
"He is our leader and right now we have to continue down the path he has set out."
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