"The authorities say our travel documents are incomplete," one of the affected women passengers said wiping her tears.
She said her family members were waiting for her in India.
The women protested at the Wagah railway station against Pakistan Railways authoritiesfor not allowing them to board the train, which runs between New Delhi and Lahore twice a week on Mondays and Thursdays.
A railway official, however, said the women could travel to Indianext on Thursday after completing their travel documents.
Samjhauta Express carrying more than100 Pakistani and 84 Indian citizens left for New Delhi amid high security. The authorities were "extra cautious" about the security today in the wake of the ongoing tension between Pakistan and India.
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Yesterday, India had conveyed to Pakistan that the train was expected to be delayed due to "internal matter" pertaining to labour.
Today, the train left Lahore for India as per schedule.
Samjhauta Express was started in 1976 between India and Pakistan.