She also said the Kartarpur corridor initiative was not linked to the dialogue process with Pakistan.
The PM said that it was the BJP government which abrogated provisions of the Article 370, while the Congress was only concerned about its "personal interests".
"On martyrdom day, I pay my respects to Bhagat Singh, Sukhdev and Rajguru who sacrificed their life for the nation," PM said in a statement.
"Peace and harmony is the only way forward to ensure a prosperous future," Dr Singh said.
At least 56 seminaries and facilities being run by JuD and its wing FIF in Pakistan's southern Sindh province have been taken over by authorities.