The Algerian government did not immediately announce the purpose of the flight but it was possible that the plane was coming to repatriate the 82-year-old leader, who has been receiving medical treatment at the University Hospitals of Geneva (HUG).
Bouteflika, in power since 1999, has rarely been seen in public since suffering a stroke in 2013.
His bid to secure a fifth term at Algeria's April 18 election has sparked massive protests in the country, dominated by youth who have called for the president to stand aside.
Bouteflika's office has insisted that the president went to Switzerland for routine medical checkups but speculation is rife that his health condition is far more serious.
On Friday, a lawyer acting on behalf of an unnamed Algerian citizen filed a petition with a Swiss court requesting that Bouteflika be placed under a trusteeship for his own protection, alleging that his "fragile health" left him vulnerable to "exploitation" by those around him.
Pointing to news reports that Bouteflika's condition was "very precarious" and "life-threatening", the petition submitted by lawyer Saskia Ditisheim also demanded that the court lift the medical secrecy around his condition and that it request a medical certificate pertaining to his aptitude to govern.
It remained unclear whether the Swiss court would admit the case, and Ditisheim acknowledged the sensitivity of the issue and told AFP the court might try to stall until Bouteflika is flown back to Algeria.
A number of protests have also been staged in Switzerland against the Algerian president since he arrived in the country.
On Friday, Algerian businessman Rachid Nekkaz, who had unsuccessfully tried to stand as a candidate in the upcoming elections, was arrested after staging a protest with several dozen supporters outside HUG and then pushing inside to demand information about Bouteflika's condition.
Nekkaz -- a popular activist with a large social media following -- suggested that Bouteflika was actually dead.
"The entire world, and all of Algeria knows that he is no longer of this world," he told reporters, charging that powerful players in Algeria had an interest in maintaining the illusion that Bouteflika was alive to keep their grip on power in the country.
Bouteflika's campaign manager Abdelghani Zaalane meanwhile insisted Thursday that the president's health raised "no worries".
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