A complaint has been filed with the Taj police by the Archaeological Survey of India.
The case was filed by Munazzar Ali, ASI caretaker of the Taj Mahal, and an FIR is yet to be recorded.
"We have ordered an inquiry. The Adlabs people had the permission (to fly the chopper) but the information could not somehow be communicated in time to the concerned agencies," said Aseem Arun, Deputy Inspector General.
He further said that it was a lack of communication and coordination.
"The film unit had the permision but information could not reach the concerned agencies in time. This is being investigated," he said.
"No, they had not taken permission from the ASI to fly over the Taj," said Indudhar Dwivedi, ASI chief, Agra.
"We did not have any information," said AK Singh, Central Industrial Security Force, which keeps a tab on the Taj's security.
"At this rate any intruder can infiltrate the high security area. Already the Taj is under threat from terrorists' groups," said Shravan Kumar Singh, heritage activist.
"This indeed is a serious matter. Our inquiries reveal they had no permission from the headquarters. The helicopter was dangerously close to the monument. I don't think any sensible person in the ASI would ever give permission. The explanation has to come from the police. We have formally lodged a complaint in the form of an FIR late in the evening at the Taj Ganj police station," said Munnazar Ali, conservation assistant, Taj Mahal
CISF sources, however, said that it was breach of security and a CISF personnel could have fired but the tragedy was averted after the district authorities informed them.
The Agra police said that they did not have any record to show that the area was a no-flying zone area.
"This is too alarming. You cannot take a risk like this. What if the helicopter developed some snag and crashed on the heritage monument or fell on visitors? Officials have now admitted that the helicopter was sighted in the no-flying zone," said Surendra Sharma, Braj Mandal Heritage Conservation Society president.
Reports reveal that the ASI had given permission to the private company to shoot aerial photographs of the monument and the Fatehpur Sikri complex by the director of monuments, ASI, New Delhi.
Indudhar Dwivedi, ASI chief in Agra, however said that no permission was granted to the private firm to fly the chopper over the Taj Mahal.