The train was delayed by nearly an hour due to the search, but traffic on the route remained unaffected, they said.
A passenger travelling in a sleeper coach of the Samata Express coming from New Delhi raised alarm after finding a suspicious note in its toilet that read "Repeatery bomb PPN in AP (sic)".
The passenger then informed Delhi Control Room, which alerted the zonal authorities who searched the train when it reached here at 10.30 am, Inspector, GRP, Pankaj Lavania said.
"The train was allowed after 50 minutes of checking in which nothing objectionable was found," he said, adding the traffic on the route remained unaffected by the delay.
"There was no other train behind Samata Express with a stoppage at Mathura junction. However, there were two trains which didn't have a halt here and continued unaffected," the PRO said.