The suspects could be questioned by US officials
The suspects were reportedly heading to Istanbul, before travelling to an Israeli city to carry out their mission.
They had been trained by, and had fought for, the Taleban in Afghanistan, police say.
The three men were detained several days ago in the eastern city of Van. Police say they had entered the country illegally from Iran.
Two of the men are said to be Palestinians, and the third a Jordanian. Police identified them as Firaz Suleiman, Ahmed Mahmoud and Mustafa Hassan.
It is the first time since the 11 September attacks that al-Qaeda suspects have been held in Turkey.
Checkpoint
Police spokesman Feyzullah Arslan told a news conference in Ankara that the suspects were arrested after their car failed to stop at a checkpoint.
He said they were members of a group, Beyyiat al-Imam, which was linked to al-Qaeda.
One of the three, named as Firaz Suleiman, had been instructed by the group to travel to an Israeli city - either Tel Aviv or Ramat Gan - and carry out the suicide mission in a "crowded area".
His two accomplices were to learn of the mission only after arriving in Jordan, said Mr Arslan.
A number of other people have also been detained in the Turkish inquiry.
'Bomb-making instructions'
One was said to have been driving the car in which the suspects were arrested. Several others were allegedly working in Istanbul to assist them.
Police did not recover any weapons or explosives, but say they found documents written in Arabic which were thought to be instructions for building a bomb.
The suspects held in Turkey could be interrogated by US officials, said one report. Turkish officials denied that a US interrogation had already taken place.
The arrests follow recent television reports which suggested that two Tunisian-born Canadians - one of whom recorded a suicide mission video found in Afghanistan - might be in Turkey.
Other police forces across Europe have arrested a number of suspects, some of them said to be key links in Osama Bin Laden's chain of command.