The IB report questions the capabilities of both the forces over detection of the drones.
It asked as to "why were they not able to detect the presence of any drone activity along their area of operation?"
The report said that Pakistani state actors were behind these incidents. It also said that the drones recovered are Chinese-made.
"The possibility of some undetected sorties has also not been ruled out," said the report, adding that on an average 10 kgs of explosives, arms or means of communication were smuggled in by the Pakistani drones.
The consignments that were smuggled into India were meant for terrorists hiding in Jammu and Kashmir.
The MHA has directed National Investigation Agency (NIA) to probe the matter and also the role of Pakistani state actors behind it. The agency after getting formal letter from MHA will register an FIR and start investigation.
Two days ago, a Pakistani drone was spotted flying over two villages in Indian territory along the India-Pakistan border in Hussainiwala area in Punjab. This was the second such incident in two days.
Villagers captured pictures of the drone on their mobile phones.
The first sighting was reported in Hazarasingh Wala village and later in Tendiwala village.
Earlier, a Pakistani drone was sighted thrice in the same area on Monday night this week.
Punjab Police has already launched elaborate investigations to account for the weapons consignments apparently smuggled into India from across the border by the two drones recovered over the last one month.
The police is probing drones spotted last month in Jhabal town in Tarn Taran district. Two drones were recovered.
Investigations so far suggest that several Pakistan-based terrorist groups were engaged in smuggling weapons into India since August, post the abrogation of Article 370 in Jammu & Kashmir.
Both the recovered drones were apparently sent by different terror groups linked with Pakistan's ISI spy agency.
( With inputs from IANS )