The JeM had taken the responsibility of the suicide attack in Jammua and Kashmir's Pulwama district on February 14, following which counter-terror action against the JeM and killed at least 350 terrorist as the IAF destroyed Pakistan-based terror outfit's biggest camp in Balakot on Tuesday.
"Regret was expressed at continuing denial by Pakistan's political and military leadership at the presence of terrorist infrastructure in territories under its control," the MEA said in a statement.
"A dossier was handed over to Pakistani side with specific details of JeM complicity in Pulwama terror attack and the presence of JeM terror camps and its leadership in Pakistan," it added.
The MEA said Pakistan was conveyed that India expects Pakistan to take immediate and verifiable action against terrorism emanating from territories under its control.
India also objected to the violation of the Indian air space by Pakistan Air Force and targeting of Indian military posts.
Meanwhile, the IAF on Wednesday chased away intruding Pakistani fighter jets in Jammu and Kashmir's Nowshera sector and shot down a Pakistani F-16 which fell on their side. Pakistan used its Air Force to target military installations in India but their attempts were foiled successfully, the MEA said, adding that India has lost one MiG 21 and one of its pilots is "missing in action" while demanding his immediate and safe return.
"It was made clear that Pakistan would be well advised to ensure that no harm comes to the Indian defence personnel in its custody. India also expects his immediate and safe return," the MEA said.