The 44-year-old, who had surgery to remove a tumour on the same gland last November, is due to remain in hospital for "three to four days" after the operation.
A statement from Barcelona's medical services revealed despite the news, Vilanova could remain in charge of the first-team squad while undergoing his treatment.
"In monitoring the process of his parotid gland, an extension of the pathology was detected, requiring surgical treatment on Thursday," the statement on fcbarcelona.es read.
"An extension of the pathology has been detected in [Vilanova's] parotid gland. The manager requires surgery which he will undergo this Thursday. He is expected to remain in hospital for three to four days.
"After the surgery, Francesc 'Tito' Vilanova will undergo chemotherapy and radiation treatment for approximately six weeks.
"During this time, and depending on how well he recovers, Vilanova's treatment may be compatible with his work life.
"Keeping in line with the patient's wishes, we urge respect and privacy during this process."
Barcelona earlier suspended their scheduled media activities for Wednesday amid reports in Spain concerning the health of Vilanova who replaced Pep Guardiola this summer.
Media reports in Spain on Wednesday morning had suggested the 44-year-old Vilanova had suffered a relapse and Barca released a press statement announcing they had suspended all activities for the day.
The statement read: "Barcelona announce that it is has suspended the press conference from president Sandro Rosell planned for midday. As well as that, the media Christmas lunch has been cancelled.
"Later today the club will issue a further release. Until that time we will not make any announcement about this matter.
"We regret any inconvenience this decision may cause."
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Vilanova took over as Barca coach as recently as April following Guardiola's decision to step down at the end of the season and take a year-long sabbatical from the game.
He was also Guardiola's assistant during four hugely successful years at the Nou Camp which saw Barca win 13 trophies, including two Champions League crowns and three La Liga titles.
Vilanova has enjoyed a superb start to his tenure in the hotseat, helping Barca establish a nine-point lead at the top of the league standings after winning 15 of their opening 16 games while drawing the other.
Barca are also through to the knockout stages of the Champions League and hold a 2-0 first-leg lead over Cordoba in their Copa del Rey last-16 tie.
Even before official confirmation from Barca about the the coach's condition, messages of support from leading figures in Spanish sport had started pouring in.
Tennis star Rafael Nadal tweeted: "All my strength and support to Tito Vilanova! We are with you to overcome this new step."
Real Betis said on their official twitter feed: "@RBetisOficial and their professionals offer their total support for the coach of @FCBarcelona_es, Tito Vilanova."
Athletic Bilbao midfielder Ander Herrera was quoted as saying in AS: "I'm stunned. Is it true? Tito has shown himself to be a fighter, overcoming a very serious illness and I hope that it's going to be the same this time. He has all of my support and that of the club."
MotoGP world champion Jorge Lorenzo, meanwhile, tweeted: "#AnimoTito (encouragement for Tito)."
Barca are away to Real Valladolid in La Liga on Saturday for their final fixture before the winter break.
Surgery will definitely rule Vilanova out of the trip with his long-term future cast into doubt given the announcement.
Reports in Spain suggest assistant manager Jordi Roura will take charge of first-team affairs during Vilanova's absence.