The agency is ending a contract with Rapiscan, the manufacturer of the scanners.
The TSA plans to continue using a scanner that is considered less invasive, producing a generic image showing where agents should look for an object on the person's body.
The TSA says the scanners will be gone by June, as Rapiscan was not able to come up with a software fix to make the scanners comply with a Congressional mandate that the scanners better protect passenger privacy.
Opponents of the scanners argue they violate basic human rights, conducting strip searches without probable cause. Advocates say the machines are efficient and faster than administering actual strip searches.