A time-bomb was found at a roadside eatery on the outskirts of the city, prompting authorities to sound an alert.
The bomb with a battery and a circuit attached to it and kept in a bag was found under a table by a waiter at around 10 p.m. on Saturday, police said.
Two youngsters who had come to eat had left behind the bag, said the staff of the joint located in Teri Bagh.
The bomb was taken in a sand-filled tractor trolley to the Kalindi Vihar forest area and defused, police said.
A team of the National Security Agency from Delhi reached Agra to assist in the investigations.
DIG (Agra) Aseem Arun said the bomb was a crude device, similar to the one which exploded at a private nursing home here in September.