"Lists of 250 civilian prisoners and 94 fishermen were handed over to Pakistan," it said.
A list of 54 Pakistani civilian prisoners and 4 fishermen, who have completed their sentence and whose nationality confirmation is awaited from Pakistan, was also handed over and Pakistan was asked to expedite the confirmation, the ministry said.
Asserting that it remains committed to addressing humanitarian matters, including those pertaining to prisoners and fishermen in each other's country, the ministry said the government has repeatedly emphasised the need for early release and repatriation of civilian prisoners, missing Indian defence personnel and fishermen along with their boats.
"We also await consular access to those Indian nationals in Pakistan's custody for whom it has so far not been provided, including Kulbhushan Jadhav and Hamid Nehal Ansari," the ministry asserted.
Pakistan has also shared a list of 58 civilian prisoners and 399 fishermen in its custody, who are Indians or believed to be Indians, it said.
The ministry said the list was exchanged between the two countries through diplomatic channels simultaneously at New Delhi and Islamabad. It was done as part of the 2008 Agreement on Consular Access between India and Pakistan.
The ministry also said a juvenile named Hasnain, whose nationality was verified by Pakistan, was being repatriated.
The exchange of the lists of prisoners comes days after Indian death-row prisoner Mr Jadhav met his family on December 25 in Islamabad.
The Jadhav-family meeting became the latest flashpoint in the already strained Indo-Pak relations with Pakistan terming its decision to allow Mr Jadhav's family to travel to Pakistan to meet him a humanitarian gesture and India accusing it of violating mutual understanding.
There was no consular access granted during Mr Jadhav's meeting with his wife and mother and instead Deputy High Commissioner JP Singh, who accompanied the two women, was initially separated from them.
They were taken to the meeting without informing Mr Singh, and the meeting was started without him, the ministry had said in a statement earlier.
Mr Singh could join only after pressing the matter with officials, but was still kept behind an additional partition that did not allow him access to the meeting as agreed.