Pakistan stopped the Samjhauta Express at the Wagah border on Thursday, citing security concerns, following which an Indian crew and guard escorted the train to Attari on the Indian side, officials said.
The train, which connects Lahore and Delhi, had 117 passengers, including 48 Pakistanis, onboard, they said.
Hundreds of passengers from both sides of the border were stuck for several hours waiting for security clearances to be completed following the disruption in the train service that connects Delhi and Lahore.
After several hours of waiting, the Samjhauta Express headed for Lahore departed from Attari at 6:41 pm with 103 passengers, including 10 Pakistanis, railway officials said.
A day after Islamabad downgraded diplomatic ties with New Delhi, Pakistan's Federal Railways Minister Sheikh Rashid Ahmed told the media in Islamabad that Pakistan has closed the Samjhauta Express train service with India.
Indian Railways officials, however, said the train has not been suspended.
"The train has not been suspended. It will run. Pakistan authorities have raised some concerns with regards to security for crew and guard of the Samjhauta Express. We have told them that the situation is normal on this side," said Northern Railway spokesperson Deepak Kumar.
"Our engine with our crew and guard escorted the train to Attari at 5:15 pm," he added.
On the Indian side, 103 passengers, including 10 Pakistanis, are waiting to cross over to Pakistan, officials said.
The train from Attari to Lahore is expected to leave Thursday evening after customary clearances.
Explaining the procedure, Kumar said the Samjhauta Express from both Lahore and Delhi come to Attari. At Attari, Delhi-bound passengers coming from Lahore get on to an Indian train. And Lahore-bound passengers board the Pakistani train that retraces its steps back to Wagah and then on to Lahore.
On Thursday, the Samjhauta Express from Lahore did not reach Attari but remained at Wagah on the Pakistan side.
The Samjhauta Express, named after the Hindi word for "agreement", comprises six sleeper coaches and an AC 3-tier coach. The train service was started on July 22, 1976, under the Simla Agreement that settled the 1971 war between the two nations.
On the Indian side, the train runs from Delhi to Attari and from Lahore to Wagah on the Pakistan side.
The Samjhauta Express train service was suspended earlier this year, due to escalating tensions between the two neighbouring countries. However, the service was later resumed.