As there were reports of two to three militants present in the Entrepreneurship Development Institute (EDI) complex, the security forces had to search all the 50 rooms of the building before calling off the operation, an army official said.
"We have recovered bodies of two militants and the search operation at the EDI building in Pampore has been almost completed," the army official said.
While one militant was killed yesterday evening, the other militant was shot dead by the security forces today, the official said.
The official said details about the slain militants were being ascertained but prima facie there were indications that they belonged to Lashkar-e-Toiba.
Security forces pounded the EDI building since Monday after the militants barged inside the complex with the aim of engaging the law enforcing agencies.
The operation, which lasted more than 56 hours, has reduced the multi-storey building to a skeleton after many of its walls were blown up.
Elite Para commandos of the army have were also called in to neutralise the militants, the official said.
The militants had stormed into the EDI complex in the wee hours of Monday and took positions inside one of the buildings.