The three were identified as Shoaib Mughal, Shahid Hussain and Humbal Akhtar.
Islamabad Police Deputy Inspector General Bin Yamin said they would soon be charged in court with terrorism offenses.
He did give specifics, but terrorism crimes can be punished by death in Pakistan. It was unclear if the men had been appointed lawyers yet.
Yamin described them as having "militant minds" and a strong hatred for America.
Pakistani-American Faisal Shahzad has pleaded guilty to terrorism and weapons charges in the United States in connection with the botched bombing.
Yamin said the three suspects had close ties to the leadership of the Pakistani Taliban, a militant group based in the northwest that has claimed responsibility for the plot.
He said the three helped Shahzad to travel to the northwest and meet militant leaders there.
They also sent him $13,000 in the United States when he ran short of money, he said.
Intelligence officers have said that up to five people were being held in connection with the plot. It is unclear what will happen to the other two.