Officials said Pakistan troops used heavy guns including Howitzer 105 mm to target civilian areas in Poonch.
An IAF official also said there have been many factually incorrect statements made by Pakistan since its aerial raid targeting Indian military installations Wednesday.
Border standoff: PM Modi reviews post-Pakistan intrusion scenario with Defence Minister, Services chiefs
The Prime Minister learnt to have discussed the evolving situation at the meeting, also attended by National Security Advisor (NSA) Ajit Doval.
Administrative officials said they have informed security agencies to investigate the matter, while defence spokesperson said the incidents in Poshal and Ratasar villages were yet to be ascertained.
The Indian Army destroyed five Pakistani posts along the Line of Control in J&K on Tuesday night in a befitting retaliation to firing from across the border.
While leaders of 21 parties were present, the Samajwadi Party did not attend the meeting. National Conference leader Omar Abdullah also skipped it.
The Union Minister also said the joint statement was being used by Pakistani media to project that the Indian polity was not united in its fight against terror.
Hope saner counsels shall prevail between leadership of India, Pakistan: Manmohan Singh on border standoff
Singh said this at a function at Teen Murti Bhavan where he was presented with the first 'P V Narasimha Rao National leadership and lifetime achievement award' by former president Pranab Mukherjee.
Pakistan Wednesday closed its airspace for commercial flights and suspended flight operations across major airports, including in Islamabad, Lahore and Karachi, for an indefinite period.
Earlier on Wednesday, AAI issued a NOTAM , saying flight operations at the airports in Srinagar, Jammu, Leh, Pathankot, Amritsar, Shimla, Kangra, Kullu Manali and Pithoragarh will remain shut.
The Indian government has acknowledged that Wing Commander Abhinandan Varthaman has been captured by the Pakistani forces and said that it expects his immediate and safe return.
Tensions between India and Pakistan rose Wednesday after Pakistan claimed it shot down two Indian fighter jets over Pakistani air space and arrested a pilot.
The firing on February 26 in Nikial and Khuiratta sectors resulted in the killing of four civilians, including three women.
'PAF shot down two Indian aircrafts inside Pakistani airspace,' tweeted military spokesman Major General Asif Ghafoor