The service connected Quetta, the capital of Pakistan's southwestern Baluchistan province, with the Iranian border town of Zahedan, said Naeem Malik, a senior official with Pakistan Railways on Wednesday.
"There were five rocket attacks on the Quetta-Zahedan track over the past 10 days," Malik said.
On Sunday, a rocket hit a train on the line, injuring a guard and damaging the locomotive, he added.
It is the only rail link between the two countries.
Pakistani authorities suspect that Baluch tribesmen have carried out the attacks as part of a campaign to compel the central government to increase payments the region receives for resources extracted there.
The tribesmen are frequently blamed for firing rockets at the rail network, gas fields and security forces, and for carrying out small scale bombings in Baluchistan.
Pakistan Railways had operated a fortnightly return passenger service and a weekly return freight service on the line until all services were suspended on Tuesday, Malik said.
He said services would remain suspended until further notice.
Malik added that the authorities also suspended a local train service between the towns of Sibi and Harnai in Baluchistan, for security reasons.
Last month, a bomb explosion on another railway line in the restive province derailed a passenger train shortly after gunmen fired on it in a mountainous region about 80km southeast of Quetta.
No one was reported hurt in the shooting or derailment.