Spain playmaker Alcantara and Austria defender Alaba — key members of the team which won the Champions League last month — are stalling over signing contract extensions with a year left on their current deals.
“The situation isn’t simple. I don’t know who will leave or join us,” admitted Flick at an event in Munich when asked about Alaba and Alcantara.
“It’s not quite ideal, but as long as both are in the squad, I am planning with them.”
Alcantara has been heavily linked to a move to the Premier League with Liverpool and Manchester United reportedly interested.
While on Spain duty last weekend, Alcantara, 29, said he had “never said that I will leave Bayern” but club bosses remain pessimistic about their chances of convincing him to stay.
After lifting the Champions League trophy in Lisbon to complete the treble, the Bayern squad returned to training on Monday to prepare for the start of the Bundesliga season at home to Schalke on September 18.
Alaba, 28, who has been linked to Manchester City, took part in online training sessions this week, and Alcantara, who was granted extra rest after playing for Spain, is also expected to take part when full training resumes Friday.
Flick insists the future of both stars must be settled soon with the new season just ten days away.
Bayern have already lost the trio of Ivan Perisic, who has returned to Inter Milan, Philippe Coutinho (Barcelona) and Alvaro Odriozola (Real Madrid) after their loan spells in Munich expired.
Perisic and Coutinho both came off the bench to play a part in the Champions League final.
“We are losing quality,” Flick said.
