The Archaeological Survey of India (ASI) order follows a gazette notification of Jan 23 and fears that rapid urbanization is threatening to wipe out valuable chunks of history, officials here said.
Under the modified rules, the power of the local ASI office to issue no objection certificates (NOCs) has been withdrawn.
"We do not know what is to be done with encroachments and structures already in existence. But in future no constructions would be permitted within the regulated zones," Superintending archaeologist A.R. Siddiqui said.
In recent years, many of the lesser known monuments in Agra have either disappeared or have been dwarfed by illegal structures.
"Most smaller protected monuments in Agra - there are scores of them - have been virtually overwhelmed by new structures which threaten their existence. These include Delhi Gate, Etmauddaula, Sikandra, Ram Bagh and dozens of others," Braj Mandal Heritage Conservation Society president Surendra Sharma said.
With land prices skyrocketing and builders making a beeline to usurp every inch of available space in the city, the survival of some of these structures has become uncertain.
Even Christian cemeteries are going off the map, their land taken over by builders and town planners.
The encroachers now threaten to gobble up Babar's Ram Bagh across the Yamuna, Mariam's tomb near Sikandra, Bagh Farzana and Begum Samru's garden -- to name a few of the relatively better known places.
Agra, home to the 17th century Taj Mahal, is India's biggest tourist draw. In the case of the Taj, no construction is allowed within 500 metres.