"We never asked for stoppage. We regret the decision to stop the rail link. It is unfortunate," Ministry of External Affairs spokesperson Raveesh Kumar, addressing a media briefing, said.
"This is part of the same narrative by Pakistan that bilateral relations have reached an alarming stage," Kumar said.
His remarks came hours after the Samjhauta Express arrived in the national capital with 117 passengers, including 76 Indian and 41 Pakistani passengers.
On Thursday, Pakistan announced that it was discontinuing the bi-weekly train that connects Lahore to Delhi, following the Indian government's decision to abrogate Article 370 that gave special status to Jammu and Kashmir.
Following Pakistan's decision, the Samjhauta Express was stranded at the Wagah border for several hours as the Pakistani crew refused to take it forward, expressing apprehension over their security in India.
The train was brought to Attari in India's Punjab after sending a locomotive and Indian crew members on Thursday evening after hours of delay.
The train was late by over four and a half hours when it chugged into the national capital.
It was earlier scheduled to arrive at the Old Delhi Railway Station at 3.35 a.m., but arrived only at 8.05 a.m.
The Samjhauta Express runs from Delhi to Attari on the Indian side and from Lahore to Wagah on the Pakistan side.
( With inputs from IANS )